Starting phenix.real_space_refine on Wed Feb 4 10:17:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkr_48335/02_2026/9mkr_48335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkr_48335/02_2026/9mkr_48335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkr_48335/02_2026/9mkr_48335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkr_48335/02_2026/9mkr_48335.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkr_48335/02_2026/9mkr_48335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkr_48335/02_2026/9mkr_48335.cif" } resolution = 3.0 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= 0.003 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 78 5.16 5 C 6228 2.51 5 N 1836 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10038 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "C" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "D" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "E" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "F" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Time building chain proxies: 2.40, per 1000 atoms: 0.24 Number of scatterers: 10038 At special positions: 0 Unit cell: (112.89, 126.67, 72.61, 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 78 16.00 O 1896 8.00 N 1836 7.00 C 6228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 190 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 214 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 523.1 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 74.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 49 through 59 removed outlier: 3.764A pdb=" N LEU A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 85 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.958A pdb=" N GLY A 92 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 136 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.009A pdb=" N SER A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.727A pdb=" N ALA A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 49 through 59 removed outlier: 3.764A pdb=" N LEU B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 85 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.958A pdb=" N GLY B 92 " --> pdb=" O PRO B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 136 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 152 through 167 Processing helix chain 'B' and resid 170 through 186 removed outlier: 4.010A pdb=" N SER B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.727A pdb=" N ALA B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 34 through 45 Processing helix chain 'C' and resid 49 through 59 removed outlier: 3.764A pdb=" N LEU C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 85 Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.958A pdb=" N GLY C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 101 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 114 through 136 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 152 through 167 Processing helix chain 'C' and resid 170 through 186 removed outlier: 4.009A pdb=" N SER C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.727A pdb=" N ALA C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 34 through 45 Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.764A pdb=" N LEU D 57 " --> pdb=" O ILE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 85 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.958A pdb=" N GLY D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 114 through 136 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 152 through 167 Processing helix chain 'D' and resid 170 through 186 removed outlier: 4.009A pdb=" N SER D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 199 Processing helix chain 'D' and resid 206 through 213 removed outlier: 3.727A pdb=" N ALA D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 34 through 45 Processing helix chain 'E' and resid 49 through 59 removed outlier: 3.764A pdb=" N LEU E 57 " --> pdb=" O ILE E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 85 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.958A pdb=" N GLY E 92 " --> pdb=" O PRO E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 101 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 114 through 136 Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 152 through 167 Processing helix chain 'E' and resid 170 through 186 removed outlier: 4.009A pdb=" N SER E 182 " --> pdb=" O LYS E 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 199 Processing helix chain 'E' and resid 206 through 213 removed outlier: 3.727A pdb=" N ALA E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 Processing helix chain 'F' and resid 34 through 45 Processing helix chain 'F' and resid 49 through 59 removed outlier: 3.764A pdb=" N LEU F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 85 Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.958A pdb=" N GLY F 92 " --> pdb=" O PRO F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 101 Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 114 through 136 Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 152 through 167 Processing helix chain 'F' and resid 170 through 186 removed outlier: 4.009A pdb=" N SER F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 206 through 213 removed outlier: 3.727A pdb=" N ALA F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=6, first strand: chain 'F' and resid 2 through 4 636 hydrogen bonds defined for protein. 1890 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: 1.49 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2540 1.33 - 1.45: 1725 1.45 - 1.57: 5809 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 10212 Sorted by residual: bond pdb=" N VAL E 15 " pdb=" CA VAL E 15 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.25e-02 6.40e+03 9.63e+00 bond pdb=" N VAL D 56 " pdb=" CA VAL D 56 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.06e-02 8.90e+03 9.54e+00 bond pdb=" N VAL A 56 " pdb=" CA VAL A 56 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.06e-02 8.90e+03 9.54e+00 bond pdb=" N VAL F 56 " pdb=" CA VAL F 56 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.06e-02 8.90e+03 9.52e+00 bond pdb=" N VAL C 56 " pdb=" CA VAL C 56 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.06e-02 8.90e+03 9.51e+00 ... (remaining 10207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 9171 1.57 - 3.14: 3831 3.14 - 4.71: 618 4.71 - 6.28: 174 6.28 - 7.85: 30 Bond angle restraints: 13824 Sorted by residual: angle pdb=" N LEU E 57 " pdb=" CA LEU E 57 " pdb=" C LEU E 57 " ideal model delta sigma weight residual 113.12 106.36 6.76 1.25e+00 6.40e-01 2.93e+01 angle pdb=" N LEU B 57 " pdb=" CA LEU B 57 " pdb=" C LEU B 57 " ideal model delta sigma weight residual 113.12 106.36 6.76 1.25e+00 6.40e-01 2.93e+01 angle pdb=" N LEU A 57 " pdb=" CA LEU A 57 " pdb=" C LEU A 57 " ideal model delta sigma weight residual 113.12 106.36 6.76 1.25e+00 6.40e-01 2.92e+01 angle pdb=" N LEU D 57 " pdb=" CA LEU D 57 " pdb=" C LEU D 57 " ideal model delta sigma weight residual 113.12 106.36 6.76 1.25e+00 6.40e-01 2.92e+01 angle pdb=" N LEU C 57 " pdb=" CA LEU C 57 " pdb=" C LEU C 57 " ideal model delta sigma weight residual 113.12 106.37 6.75 1.25e+00 6.40e-01 2.91e+01 ... (remaining 13819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.05: 5995 12.05 - 24.09: 167 24.09 - 36.14: 114 36.14 - 48.19: 12 48.19 - 60.24: 54 Dihedral angle restraints: 6342 sinusoidal: 2610 harmonic: 3732 Sorted by residual: dihedral pdb=" CB CYS A 190 " pdb=" SG CYS A 190 " pdb=" SG CYS A 214 " pdb=" CB CYS A 214 " ideal model delta sinusoidal sigma weight residual 93.00 124.33 -31.33 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CB CYS D 190 " pdb=" SG CYS D 190 " pdb=" SG CYS D 214 " pdb=" CB CYS D 214 " ideal model delta sinusoidal sigma weight residual 93.00 124.33 -31.33 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CB CYS C 190 " pdb=" SG CYS C 190 " pdb=" SG CYS C 214 " pdb=" CB CYS C 214 " ideal model delta sinusoidal sigma weight residual 93.00 124.33 -31.33 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 6339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 558 0.056 - 0.112: 504 0.112 - 0.168: 284 0.168 - 0.224: 146 0.224 - 0.281: 26 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA VAL E 33 " pdb=" N VAL E 33 " pdb=" C VAL E 33 " pdb=" CB VAL E 33 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA VAL B 33 " pdb=" N VAL B 33 " pdb=" C VAL B 33 " pdb=" CB VAL B 33 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA VAL D 33 " pdb=" N VAL D 33 " pdb=" C VAL D 33 " pdb=" CB VAL D 33 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1515 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 124 " -0.024 2.00e-02 2.50e+03 1.79e-02 7.98e+00 pdb=" CG TRP C 124 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 124 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 124 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP C 124 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 124 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 124 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 124 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 124 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 124 " 0.024 2.00e-02 2.50e+03 1.78e-02 7.96e+00 pdb=" CG TRP F 124 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 124 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP F 124 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP F 124 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 124 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 124 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 124 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 124 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP F 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 124 " -0.024 2.00e-02 2.50e+03 1.78e-02 7.96e+00 pdb=" CG TRP E 124 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP E 124 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 124 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP E 124 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 124 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 124 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 124 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 124 " -0.016 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3843 2.87 - 3.38: 11209 3.38 - 3.89: 17350 3.89 - 4.39: 21067 4.39 - 4.90: 32480 Nonbonded interactions: 85949 Sorted by model distance: nonbonded pdb=" OH TYR F 153 " pdb=" OG SER F 182 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR D 153 " pdb=" OG SER D 182 " model vdw 2.366 3.040 nonbonded pdb=" OH TYR A 153 " pdb=" OG SER A 182 " model vdw 2.366 3.040 nonbonded pdb=" OH TYR E 153 " pdb=" OG SER E 182 " model vdw 2.366 3.040 nonbonded pdb=" OH TYR B 153 " pdb=" OG SER B 182 " model vdw 2.366 3.040 ... (remaining 85944 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.044 10218 Z= 0.952 Angle : 1.698 7.854 13836 Z= 1.298 Chirality : 0.105 0.281 1518 Planarity : 0.009 0.111 1842 Dihedral : 9.976 60.236 3900 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.57 % Allowed : 2.27 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.25), residues: 1272 helix: 0.46 (0.18), residues: 930 sheet: 0.61 (0.65), residues: 54 loop : 0.59 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 159 TYR 0.010 0.002 TYR B 43 PHE 0.011 0.003 PHE B 156 TRP 0.037 0.006 TRP F 124 HIS 0.005 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.01276 (10212) covalent geometry : angle 1.69724 (13824) SS BOND : bond 0.00069 ( 6) SS BOND : angle 2.10980 ( 12) hydrogen bonds : bond 0.21441 ( 636) hydrogen bonds : angle 7.00668 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 540 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.7906 (ttpp) cc_final: 0.7206 (ttpp) REVERT: A 161 LEU cc_start: 0.9167 (mt) cc_final: 0.8933 (mm) REVERT: B 13 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7265 (ttpp) REVERT: B 161 LEU cc_start: 0.9172 (mt) cc_final: 0.8881 (mm) REVERT: C 13 LYS cc_start: 0.7886 (ttpp) cc_final: 0.7367 (ttpp) REVERT: C 161 LEU cc_start: 0.9164 (mt) cc_final: 0.8916 (mm) REVERT: D 13 LYS cc_start: 0.7914 (ttpp) cc_final: 0.7226 (ttpp) REVERT: D 161 LEU cc_start: 0.9166 (mt) cc_final: 0.8934 (mm) REVERT: E 13 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7241 (ttpp) REVERT: E 161 LEU cc_start: 0.9171 (mt) cc_final: 0.8881 (mm) REVERT: F 13 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7382 (ttpp) REVERT: F 161 LEU cc_start: 0.9160 (mt) cc_final: 0.8915 (mm) outliers start: 6 outliers final: 0 residues processed: 546 average time/residue: 0.5369 time to fit residues: 313.9851 Evaluate side-chains 332 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 71 GLN ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 40 GLN B 71 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN D 40 GLN D 71 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN E 40 GLN E 71 GLN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN F 40 GLN F 71 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.085869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059275 restraints weight = 31515.714| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.67 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10218 Z= 0.220 Angle : 0.858 9.481 13836 Z= 0.458 Chirality : 0.043 0.154 1518 Planarity : 0.005 0.036 1842 Dihedral : 4.422 15.901 1386 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.27 % Allowed : 23.39 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.23), residues: 1272 helix: 0.79 (0.17), residues: 900 sheet: 0.21 (0.56), residues: 54 loop : 0.11 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 159 TYR 0.029 0.004 TYR A 183 PHE 0.035 0.003 PHE D 156 TRP 0.024 0.004 TRP A 81 HIS 0.009 0.002 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00503 (10212) covalent geometry : angle 0.85835 (13824) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.51329 ( 12) hydrogen bonds : bond 0.06119 ( 636) hydrogen bonds : angle 5.52447 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 339 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TRP cc_start: 0.8436 (t60) cc_final: 0.7954 (t60) REVERT: A 19 MET cc_start: 0.8167 (tmm) cc_final: 0.7894 (tmm) REVERT: A 143 MET cc_start: 0.8655 (mpp) cc_final: 0.8449 (mpp) REVERT: A 156 PHE cc_start: 0.9223 (t80) cc_final: 0.8920 (t80) REVERT: A 165 ASP cc_start: 0.9168 (m-30) cc_final: 0.8942 (p0) REVERT: A 183 TYR cc_start: 0.9597 (t80) cc_final: 0.9209 (t80) REVERT: B 12 TRP cc_start: 0.8349 (t60) cc_final: 0.8079 (t60) REVERT: B 97 ASP cc_start: 0.9496 (m-30) cc_final: 0.9053 (t0) REVERT: B 106 ASN cc_start: 0.8361 (t0) cc_final: 0.8130 (t0) REVERT: B 135 MET cc_start: 0.9363 (ptm) cc_final: 0.9058 (ptm) REVERT: B 143 MET cc_start: 0.8665 (mpp) cc_final: 0.8408 (mpp) REVERT: B 165 ASP cc_start: 0.9231 (m-30) cc_final: 0.8856 (p0) REVERT: B 174 LYS cc_start: 0.9439 (mtpt) cc_final: 0.9221 (mtpp) REVERT: B 183 TYR cc_start: 0.9562 (t80) cc_final: 0.9242 (t80) REVERT: C 12 TRP cc_start: 0.8351 (t60) cc_final: 0.8097 (t60) REVERT: C 19 MET cc_start: 0.8103 (tmm) cc_final: 0.7826 (tmm) REVERT: C 106 ASN cc_start: 0.8383 (t0) cc_final: 0.8145 (t0) REVERT: C 143 MET cc_start: 0.8687 (mpp) cc_final: 0.8444 (mpp) REVERT: C 165 ASP cc_start: 0.9175 (m-30) cc_final: 0.8909 (p0) REVERT: C 183 TYR cc_start: 0.9603 (t80) cc_final: 0.9228 (t80) REVERT: D 12 TRP cc_start: 0.8443 (t60) cc_final: 0.7958 (t60) REVERT: D 19 MET cc_start: 0.8162 (tmm) cc_final: 0.7889 (tmm) REVERT: D 143 MET cc_start: 0.8656 (mpp) cc_final: 0.8450 (mpp) REVERT: D 156 PHE cc_start: 0.9213 (t80) cc_final: 0.8912 (t80) REVERT: D 165 ASP cc_start: 0.9167 (m-30) cc_final: 0.8939 (p0) REVERT: D 183 TYR cc_start: 0.9596 (t80) cc_final: 0.9211 (t80) REVERT: E 12 TRP cc_start: 0.8349 (t60) cc_final: 0.8079 (t60) REVERT: E 36 ASP cc_start: 0.9008 (m-30) cc_final: 0.8704 (m-30) REVERT: E 97 ASP cc_start: 0.9479 (m-30) cc_final: 0.9034 (t0) REVERT: E 106 ASN cc_start: 0.8358 (t0) cc_final: 0.8121 (t0) REVERT: E 135 MET cc_start: 0.9353 (ptm) cc_final: 0.9046 (ptm) REVERT: E 143 MET cc_start: 0.8670 (mpp) cc_final: 0.8415 (mpp) REVERT: E 165 ASP cc_start: 0.9233 (m-30) cc_final: 0.8999 (p0) REVERT: E 174 LYS cc_start: 0.9437 (mtpt) cc_final: 0.9219 (mtpp) REVERT: E 183 TYR cc_start: 0.9560 (t80) cc_final: 0.9234 (t80) REVERT: F 12 TRP cc_start: 0.8356 (t60) cc_final: 0.8102 (t60) REVERT: F 19 MET cc_start: 0.8089 (tmm) cc_final: 0.7815 (tmm) REVERT: F 106 ASN cc_start: 0.8393 (t0) cc_final: 0.8157 (t0) REVERT: F 143 MET cc_start: 0.8686 (mpp) cc_final: 0.8443 (mpp) REVERT: F 165 ASP cc_start: 0.9177 (m-30) cc_final: 0.8912 (p0) REVERT: F 183 TYR cc_start: 0.9610 (t80) cc_final: 0.9310 (t80) outliers start: 24 outliers final: 6 residues processed: 351 average time/residue: 0.4717 time to fit residues: 178.8044 Evaluate side-chains 314 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 308 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN B 106 ASN B 123 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN C 40 GLN C 106 ASN C 123 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN E 106 ASN E 123 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 106 ASN F 123 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.083982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.056608 restraints weight = 32021.398| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.81 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10218 Z= 0.224 Angle : 0.830 14.913 13836 Z= 0.420 Chirality : 0.042 0.205 1518 Planarity : 0.005 0.045 1842 Dihedral : 4.334 15.966 1386 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.98 % Allowed : 24.72 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.23), residues: 1272 helix: 1.39 (0.17), residues: 858 sheet: 0.31 (0.54), residues: 54 loop : 0.21 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 130 TYR 0.022 0.002 TYR D 153 PHE 0.026 0.003 PHE C 156 TRP 0.019 0.003 TRP B 81 HIS 0.009 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00521 (10212) covalent geometry : angle 0.83046 (13824) SS BOND : bond 0.00110 ( 6) SS BOND : angle 0.23795 ( 12) hydrogen bonds : bond 0.05338 ( 636) hydrogen bonds : angle 5.25100 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8341 (tmm) cc_final: 0.8003 (tmm) REVERT: A 68 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8567 (tm-30) REVERT: A 76 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9014 (tm-30) REVERT: A 77 GLU cc_start: 0.9024 (tt0) cc_final: 0.8297 (tm-30) REVERT: A 106 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8723 (t0) REVERT: A 143 MET cc_start: 0.8800 (mpp) cc_final: 0.8597 (mpp) REVERT: A 156 PHE cc_start: 0.9224 (t80) cc_final: 0.8913 (t80) REVERT: A 183 TYR cc_start: 0.9594 (t80) cc_final: 0.9158 (t80) REVERT: A 211 MET cc_start: 0.8751 (mtp) cc_final: 0.8498 (mtp) REVERT: B 154 GLU cc_start: 0.9282 (pm20) cc_final: 0.9042 (pm20) REVERT: B 183 TYR cc_start: 0.9571 (t80) cc_final: 0.9284 (t80) REVERT: C 19 MET cc_start: 0.8294 (tmm) cc_final: 0.7853 (tmm) REVERT: C 143 MET cc_start: 0.8954 (mpp) cc_final: 0.8742 (mpp) REVERT: C 183 TYR cc_start: 0.9612 (t80) cc_final: 0.9248 (t80) REVERT: D 19 MET cc_start: 0.8340 (tmm) cc_final: 0.8003 (tmm) REVERT: D 68 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8738 (tm-30) REVERT: D 76 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9013 (tm-30) REVERT: D 77 GLU cc_start: 0.9021 (tt0) cc_final: 0.8298 (tm-30) REVERT: D 106 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8701 (t0) REVERT: D 143 MET cc_start: 0.8803 (mpp) cc_final: 0.8600 (mpp) REVERT: D 156 PHE cc_start: 0.9223 (t80) cc_final: 0.8908 (t80) REVERT: D 183 TYR cc_start: 0.9594 (t80) cc_final: 0.9160 (t80) REVERT: D 211 MET cc_start: 0.8757 (mtp) cc_final: 0.8504 (mtp) REVERT: E 183 TYR cc_start: 0.9571 (t80) cc_final: 0.9284 (t80) REVERT: F 19 MET cc_start: 0.8286 (tmm) cc_final: 0.7843 (tmm) REVERT: F 143 MET cc_start: 0.8954 (mpp) cc_final: 0.8743 (mpp) REVERT: F 207 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9092 (p) outliers start: 42 outliers final: 19 residues processed: 324 average time/residue: 0.4452 time to fit residues: 155.9012 Evaluate side-chains 289 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.082875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.055292 restraints weight = 32696.546| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.66 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10218 Z= 0.173 Angle : 0.797 11.680 13836 Z= 0.407 Chirality : 0.048 0.411 1518 Planarity : 0.005 0.051 1842 Dihedral : 4.390 16.270 1386 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 3.03 % Allowed : 26.42 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1272 helix: 1.29 (0.17), residues: 882 sheet: 0.20 (0.50), residues: 54 loop : -0.06 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 130 TYR 0.034 0.003 TYR A 153 PHE 0.024 0.003 PHE F 156 TRP 0.019 0.002 TRP B 81 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00381 (10212) covalent geometry : angle 0.79762 (13824) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.32851 ( 12) hydrogen bonds : bond 0.05065 ( 636) hydrogen bonds : angle 5.02838 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8652 (tm-30) REVERT: A 76 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9058 (tm-30) REVERT: A 77 GLU cc_start: 0.9060 (tt0) cc_final: 0.8302 (tm-30) REVERT: A 124 TRP cc_start: 0.9510 (m-10) cc_final: 0.8844 (m-10) REVERT: A 203 GLN cc_start: 0.9006 (pm20) cc_final: 0.8374 (mp10) REVERT: A 209 GLU cc_start: 0.9311 (mp0) cc_final: 0.8671 (mp0) REVERT: B 35 GLU cc_start: 0.8528 (pm20) cc_final: 0.8294 (pm20) REVERT: B 36 ASP cc_start: 0.8845 (m-30) cc_final: 0.8547 (m-30) REVERT: B 183 TYR cc_start: 0.9565 (t80) cc_final: 0.9245 (t80) REVERT: C 19 MET cc_start: 0.8262 (tmm) cc_final: 0.7911 (tmm) REVERT: C 143 MET cc_start: 0.9003 (mpp) cc_final: 0.8784 (mpp) REVERT: C 183 TYR cc_start: 0.9576 (t80) cc_final: 0.9132 (t80) REVERT: D 68 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8813 (tm-30) REVERT: D 76 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9054 (tm-30) REVERT: D 77 GLU cc_start: 0.9058 (tt0) cc_final: 0.8305 (tm-30) REVERT: D 124 TRP cc_start: 0.9510 (m-10) cc_final: 0.8845 (m-10) REVERT: D 203 GLN cc_start: 0.9010 (pm20) cc_final: 0.8375 (mp10) REVERT: D 209 GLU cc_start: 0.9311 (mp0) cc_final: 0.8694 (mp0) REVERT: E 35 GLU cc_start: 0.8754 (pm20) cc_final: 0.8331 (pm20) REVERT: E 183 TYR cc_start: 0.9562 (t80) cc_final: 0.9241 (t80) REVERT: F 19 MET cc_start: 0.8267 (tmm) cc_final: 0.7918 (tmm) REVERT: F 143 MET cc_start: 0.9005 (mpp) cc_final: 0.8787 (mpp) outliers start: 32 outliers final: 19 residues processed: 335 average time/residue: 0.5116 time to fit residues: 184.4153 Evaluate side-chains 310 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 0.0470 chunk 101 optimal weight: 4.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.082609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054636 restraints weight = 32520.036| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.65 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10218 Z= 0.173 Angle : 0.831 13.929 13836 Z= 0.415 Chirality : 0.050 0.448 1518 Planarity : 0.005 0.050 1842 Dihedral : 4.457 19.665 1386 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 3.50 % Allowed : 26.70 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.23), residues: 1272 helix: 1.41 (0.17), residues: 846 sheet: -0.07 (0.48), residues: 54 loop : 0.05 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 130 TYR 0.020 0.002 TYR A 153 PHE 0.014 0.002 PHE A 156 TRP 0.018 0.002 TRP B 81 HIS 0.002 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00394 (10212) covalent geometry : angle 0.83090 (13824) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.17137 ( 12) hydrogen bonds : bond 0.04885 ( 636) hydrogen bonds : angle 5.06458 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 309 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8278 (tmm) cc_final: 0.8020 (tmm) REVERT: A 28 MET cc_start: 0.9342 (tpp) cc_final: 0.9127 (tpt) REVERT: A 35 GLU cc_start: 0.8530 (pm20) cc_final: 0.8326 (pm20) REVERT: A 36 ASP cc_start: 0.8877 (m-30) cc_final: 0.8611 (m-30) REVERT: A 76 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8917 (tm-30) REVERT: A 79 GLU cc_start: 0.9191 (pp20) cc_final: 0.8760 (pp20) REVERT: A 167 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 198 LEU cc_start: 0.8693 (mt) cc_final: 0.8493 (pp) REVERT: A 203 GLN cc_start: 0.9038 (pm20) cc_final: 0.8562 (mp10) REVERT: B 19 MET cc_start: 0.8271 (tmm) cc_final: 0.8066 (tmm) REVERT: B 35 GLU cc_start: 0.8554 (pm20) cc_final: 0.8241 (pm20) REVERT: B 36 ASP cc_start: 0.8853 (m-30) cc_final: 0.8476 (m-30) REVERT: B 183 TYR cc_start: 0.9563 (t80) cc_final: 0.9152 (t80) REVERT: B 198 LEU cc_start: 0.8680 (mt) cc_final: 0.8363 (pp) REVERT: B 203 GLN cc_start: 0.8978 (pm20) cc_final: 0.8362 (mp10) REVERT: B 209 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8847 (mp0) REVERT: C 19 MET cc_start: 0.8343 (tmm) cc_final: 0.8038 (tmm) REVERT: C 35 GLU cc_start: 0.8469 (pm20) cc_final: 0.8224 (pm20) REVERT: C 36 ASP cc_start: 0.8857 (m-30) cc_final: 0.8599 (m-30) REVERT: C 143 MET cc_start: 0.9085 (mpp) cc_final: 0.8840 (mpp) REVERT: C 198 LEU cc_start: 0.8767 (mt) cc_final: 0.8521 (pp) REVERT: D 19 MET cc_start: 0.8277 (tmm) cc_final: 0.8019 (tmm) REVERT: D 28 MET cc_start: 0.9342 (tpp) cc_final: 0.9125 (tpt) REVERT: D 35 GLU cc_start: 0.8530 (pm20) cc_final: 0.8326 (pm20) REVERT: D 36 ASP cc_start: 0.8869 (m-30) cc_final: 0.8604 (m-30) REVERT: D 76 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8938 (tm-30) REVERT: D 79 GLU cc_start: 0.9203 (pp20) cc_final: 0.8774 (pp20) REVERT: D 167 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7432 (mm-30) REVERT: D 198 LEU cc_start: 0.8699 (mt) cc_final: 0.8498 (pp) REVERT: D 203 GLN cc_start: 0.9042 (pm20) cc_final: 0.8565 (mp10) REVERT: E 19 MET cc_start: 0.8274 (tmm) cc_final: 0.8066 (tmm) REVERT: E 35 GLU cc_start: 0.8813 (pm20) cc_final: 0.8458 (pm20) REVERT: E 183 TYR cc_start: 0.9562 (t80) cc_final: 0.9155 (t80) REVERT: E 198 LEU cc_start: 0.8699 (mt) cc_final: 0.8382 (pp) REVERT: F 19 MET cc_start: 0.8339 (tmm) cc_final: 0.8030 (tmm) REVERT: F 36 ASP cc_start: 0.8854 (m-30) cc_final: 0.8605 (m-30) REVERT: F 143 MET cc_start: 0.9090 (mpp) cc_final: 0.8849 (mpp) outliers start: 37 outliers final: 21 residues processed: 326 average time/residue: 0.5205 time to fit residues: 182.7925 Evaluate side-chains 292 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 271 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN E 134 HIS ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.080432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052676 restraints weight = 32893.764| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.59 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10218 Z= 0.239 Angle : 0.853 15.478 13836 Z= 0.427 Chirality : 0.049 0.445 1518 Planarity : 0.005 0.051 1842 Dihedral : 4.398 20.140 1386 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.60 % Allowed : 28.98 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.23), residues: 1272 helix: 1.16 (0.17), residues: 882 sheet: -0.50 (0.50), residues: 54 loop : -0.41 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 130 TYR 0.027 0.002 TYR B 153 PHE 0.014 0.003 PHE B 156 TRP 0.029 0.003 TRP A 124 HIS 0.003 0.001 HIS F 30 Details of bonding type rmsd covalent geometry : bond 0.00550 (10212) covalent geometry : angle 0.85329 (13824) SS BOND : bond 0.00098 ( 6) SS BOND : angle 0.13492 ( 12) hydrogen bonds : bond 0.04888 ( 636) hydrogen bonds : angle 5.13979 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8409 (tmm) cc_final: 0.7999 (tmm) REVERT: A 28 MET cc_start: 0.9351 (tpp) cc_final: 0.9146 (tpt) REVERT: A 34 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7269 (m) REVERT: A 35 GLU cc_start: 0.8405 (pm20) cc_final: 0.8151 (tt0) REVERT: A 76 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8962 (tm-30) REVERT: A 77 GLU cc_start: 0.9059 (tt0) cc_final: 0.8537 (tm-30) REVERT: A 79 GLU cc_start: 0.9219 (pp20) cc_final: 0.8786 (pp20) REVERT: A 167 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 203 GLN cc_start: 0.9030 (pm20) cc_final: 0.8605 (mp10) REVERT: B 19 MET cc_start: 0.8389 (tmm) cc_final: 0.8142 (tmm) REVERT: B 36 ASP cc_start: 0.8751 (m-30) cc_final: 0.8415 (m-30) REVERT: B 198 LEU cc_start: 0.8804 (mt) cc_final: 0.8500 (pp) REVERT: B 203 GLN cc_start: 0.8990 (pm20) cc_final: 0.8441 (mp10) REVERT: C 19 MET cc_start: 0.8485 (tmm) cc_final: 0.7994 (tmm) REVERT: C 36 ASP cc_start: 0.8753 (m-30) cc_final: 0.8543 (m-30) REVERT: C 143 MET cc_start: 0.9097 (mpp) cc_final: 0.8865 (mpp) REVERT: C 198 LEU cc_start: 0.8933 (mt) cc_final: 0.8684 (pp) REVERT: C 203 GLN cc_start: 0.8968 (pm20) cc_final: 0.8392 (mp10) REVERT: D 19 MET cc_start: 0.8400 (tmm) cc_final: 0.7989 (tmm) REVERT: D 28 MET cc_start: 0.9348 (tpp) cc_final: 0.9139 (tpt) REVERT: D 76 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8975 (tm-30) REVERT: D 77 GLU cc_start: 0.9064 (tt0) cc_final: 0.8557 (tm-30) REVERT: D 79 GLU cc_start: 0.9231 (pp20) cc_final: 0.8802 (pp20) REVERT: D 167 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7504 (mm-30) REVERT: D 203 GLN cc_start: 0.9034 (pm20) cc_final: 0.8610 (mp10) REVERT: E 19 MET cc_start: 0.8400 (tmm) cc_final: 0.8144 (tmm) REVERT: E 35 GLU cc_start: 0.8858 (pm20) cc_final: 0.8541 (pm20) REVERT: E 198 LEU cc_start: 0.8808 (mt) cc_final: 0.8499 (pp) REVERT: E 203 GLN cc_start: 0.8988 (pm20) cc_final: 0.8432 (mp10) REVERT: F 19 MET cc_start: 0.8494 (tmm) cc_final: 0.7999 (tmm) REVERT: F 143 MET cc_start: 0.9101 (mpp) cc_final: 0.8870 (mpp) REVERT: F 203 GLN cc_start: 0.8962 (pm20) cc_final: 0.8379 (mp10) outliers start: 38 outliers final: 23 residues processed: 297 average time/residue: 0.5115 time to fit residues: 163.4332 Evaluate side-chains 290 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.081808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053759 restraints weight = 32029.885| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.54 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10218 Z= 0.166 Angle : 0.870 16.319 13836 Z= 0.426 Chirality : 0.049 0.461 1518 Planarity : 0.005 0.055 1842 Dihedral : 4.420 19.003 1386 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.22 % Allowed : 29.83 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.23), residues: 1272 helix: 1.17 (0.18), residues: 852 sheet: -0.36 (0.48), residues: 54 loop : -0.32 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 201 TYR 0.020 0.002 TYR B 183 PHE 0.011 0.002 PHE C 156 TRP 0.033 0.003 TRP F 124 HIS 0.002 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00372 (10212) covalent geometry : angle 0.86990 (13824) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.17435 ( 12) hydrogen bonds : bond 0.04830 ( 636) hydrogen bonds : angle 5.00989 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8403 (tmm) cc_final: 0.8028 (tmm) REVERT: A 28 MET cc_start: 0.9336 (tpp) cc_final: 0.9132 (tpt) REVERT: A 59 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8167 (mtp) REVERT: A 76 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8978 (tm-30) REVERT: A 77 GLU cc_start: 0.9106 (tt0) cc_final: 0.8579 (tm-30) REVERT: A 79 GLU cc_start: 0.9233 (pp20) cc_final: 0.8754 (pp20) REVERT: A 167 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 202 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8306 (p) REVERT: A 203 GLN cc_start: 0.9036 (pm20) cc_final: 0.8634 (mp10) REVERT: B 28 MET cc_start: 0.9322 (tpp) cc_final: 0.9107 (tpt) REVERT: B 198 LEU cc_start: 0.8911 (mt) cc_final: 0.8594 (pp) REVERT: B 203 GLN cc_start: 0.8972 (pm20) cc_final: 0.8510 (mp10) REVERT: C 19 MET cc_start: 0.8489 (tmm) cc_final: 0.8103 (tmm) REVERT: C 143 MET cc_start: 0.9122 (mpp) cc_final: 0.8883 (mpp) REVERT: C 179 LEU cc_start: 0.9604 (mm) cc_final: 0.9246 (tp) REVERT: C 198 LEU cc_start: 0.9126 (mt) cc_final: 0.8599 (pp) REVERT: C 203 GLN cc_start: 0.8961 (pm20) cc_final: 0.8143 (mp10) REVERT: D 19 MET cc_start: 0.8400 (tmm) cc_final: 0.8024 (tmm) REVERT: D 34 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.6913 (m) REVERT: D 36 ASP cc_start: 0.9085 (m-30) cc_final: 0.8722 (p0) REVERT: D 59 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8183 (mtp) REVERT: D 76 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8988 (tm-30) REVERT: D 77 GLU cc_start: 0.9106 (tt0) cc_final: 0.8429 (tm-30) REVERT: D 79 GLU cc_start: 0.9240 (pp20) cc_final: 0.8776 (pp20) REVERT: D 124 TRP cc_start: 0.9477 (m-10) cc_final: 0.9083 (m-10) REVERT: D 167 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7433 (mm-30) REVERT: D 202 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8269 (p) REVERT: D 203 GLN cc_start: 0.9033 (pm20) cc_final: 0.8628 (mp10) REVERT: E 28 MET cc_start: 0.9326 (tpp) cc_final: 0.9120 (tpt) REVERT: E 35 GLU cc_start: 0.8824 (pm20) cc_final: 0.8489 (pm20) REVERT: E 198 LEU cc_start: 0.8908 (mt) cc_final: 0.8590 (pp) REVERT: E 203 GLN cc_start: 0.8975 (pm20) cc_final: 0.8507 (mp10) REVERT: F 19 MET cc_start: 0.8499 (tmm) cc_final: 0.8145 (tmm) REVERT: F 35 GLU cc_start: 0.8757 (pm20) cc_final: 0.8530 (pm20) REVERT: F 143 MET cc_start: 0.9124 (mpp) cc_final: 0.8885 (mpp) REVERT: F 179 LEU cc_start: 0.9593 (mm) cc_final: 0.9233 (tp) REVERT: F 203 GLN cc_start: 0.8980 (pm20) cc_final: 0.8131 (mp10) outliers start: 34 outliers final: 18 residues processed: 314 average time/residue: 0.5428 time to fit residues: 183.1474 Evaluate side-chains 286 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 263 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 111 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 35 optimal weight: 7.9990 chunk 92 optimal weight: 0.0010 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 40 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.082758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055266 restraints weight = 31892.984| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.49 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10218 Z= 0.166 Angle : 0.928 16.256 13836 Z= 0.450 Chirality : 0.050 0.483 1518 Planarity : 0.005 0.055 1842 Dihedral : 4.399 18.935 1386 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.94 % Allowed : 32.39 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.23), residues: 1272 helix: 1.11 (0.18), residues: 846 sheet: -0.28 (0.47), residues: 54 loop : -0.38 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 201 TYR 0.026 0.002 TYR E 153 PHE 0.010 0.002 PHE E 156 TRP 0.036 0.003 TRP F 124 HIS 0.002 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00362 (10212) covalent geometry : angle 0.92805 (13824) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.14703 ( 12) hydrogen bonds : bond 0.04730 ( 636) hydrogen bonds : angle 5.03746 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8343 (tmm) cc_final: 0.7856 (tmm) REVERT: A 28 MET cc_start: 0.9337 (tpp) cc_final: 0.9119 (tpt) REVERT: A 59 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8061 (mtp) REVERT: A 68 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8760 (pp20) REVERT: A 76 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8989 (tm-30) REVERT: A 77 GLU cc_start: 0.9109 (tt0) cc_final: 0.8550 (tm-30) REVERT: A 79 GLU cc_start: 0.9246 (pp20) cc_final: 0.8764 (pp20) REVERT: A 124 TRP cc_start: 0.9466 (m-10) cc_final: 0.8618 (m-10) REVERT: A 167 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 202 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8285 (m) REVERT: A 203 GLN cc_start: 0.9044 (pm20) cc_final: 0.8710 (mp10) REVERT: A 210 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8682 (mmtt) REVERT: B 35 GLU cc_start: 0.8541 (mp0) cc_final: 0.8260 (mp0) REVERT: B 198 LEU cc_start: 0.8961 (mt) cc_final: 0.8627 (pp) REVERT: B 203 GLN cc_start: 0.8990 (pm20) cc_final: 0.8565 (mp10) REVERT: C 19 MET cc_start: 0.8391 (tmm) cc_final: 0.8066 (tmm) REVERT: C 68 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8959 (tm-30) REVERT: C 143 MET cc_start: 0.9138 (mpp) cc_final: 0.8894 (mpp) REVERT: C 179 LEU cc_start: 0.9598 (mm) cc_final: 0.9244 (tp) REVERT: C 198 LEU cc_start: 0.9181 (mt) cc_final: 0.8641 (pp) REVERT: D 19 MET cc_start: 0.8326 (tmm) cc_final: 0.7839 (tmm) REVERT: D 59 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8071 (mtp) REVERT: D 76 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9011 (tm-30) REVERT: D 77 GLU cc_start: 0.9110 (tt0) cc_final: 0.8599 (tm-30) REVERT: D 79 GLU cc_start: 0.9241 (pp20) cc_final: 0.8764 (pp20) REVERT: D 167 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 202 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8285 (m) REVERT: D 203 GLN cc_start: 0.9048 (pm20) cc_final: 0.8716 (mp10) REVERT: D 210 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8677 (mmtt) REVERT: E 35 GLU cc_start: 0.8820 (pm20) cc_final: 0.8487 (pm20) REVERT: E 68 GLU cc_start: 0.9327 (tm-30) cc_final: 0.9103 (tm-30) REVERT: E 198 LEU cc_start: 0.8958 (mt) cc_final: 0.8654 (pp) REVERT: E 203 GLN cc_start: 0.8981 (pm20) cc_final: 0.8556 (mp10) REVERT: E 209 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8782 (mp0) REVERT: F 19 MET cc_start: 0.8377 (tmm) cc_final: 0.8090 (tmm) REVERT: F 143 MET cc_start: 0.9141 (mpp) cc_final: 0.8897 (mpp) REVERT: F 179 LEU cc_start: 0.9594 (mm) cc_final: 0.9230 (tp) REVERT: F 203 GLN cc_start: 0.8991 (pm20) cc_final: 0.8136 (mp10) outliers start: 31 outliers final: 18 residues processed: 311 average time/residue: 0.5102 time to fit residues: 170.3117 Evaluate side-chains 288 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN D 21 GLN D 123 GLN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.082023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054469 restraints weight = 32248.202| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.55 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10218 Z= 0.189 Angle : 0.948 15.632 13836 Z= 0.458 Chirality : 0.050 0.462 1518 Planarity : 0.005 0.056 1842 Dihedral : 4.379 20.598 1386 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.27 % Allowed : 34.66 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.23), residues: 1272 helix: 1.01 (0.18), residues: 852 sheet: -0.44 (0.48), residues: 54 loop : -0.31 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 201 TYR 0.019 0.002 TYR A 153 PHE 0.010 0.002 PHE D 37 TRP 0.035 0.003 TRP B 124 HIS 0.002 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00428 (10212) covalent geometry : angle 0.94812 (13824) SS BOND : bond 0.00226 ( 6) SS BOND : angle 0.10620 ( 12) hydrogen bonds : bond 0.04800 ( 636) hydrogen bonds : angle 5.13091 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8376 (tmm) cc_final: 0.7905 (tmm) REVERT: A 28 MET cc_start: 0.9345 (tpp) cc_final: 0.9124 (tpt) REVERT: A 76 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9015 (tm-30) REVERT: A 79 GLU cc_start: 0.9247 (pp20) cc_final: 0.8752 (pp20) REVERT: A 154 GLU cc_start: 0.9073 (pm20) cc_final: 0.8868 (pm20) REVERT: A 167 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 202 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8404 (m) REVERT: A 203 GLN cc_start: 0.9055 (pm20) cc_final: 0.8758 (mp10) REVERT: B 35 GLU cc_start: 0.8644 (mp0) cc_final: 0.8262 (mp0) REVERT: B 76 GLU cc_start: 0.9239 (mp0) cc_final: 0.8982 (mp0) REVERT: B 179 LEU cc_start: 0.9555 (mm) cc_final: 0.9280 (tt) REVERT: B 198 LEU cc_start: 0.9224 (mt) cc_final: 0.8660 (pp) REVERT: B 203 GLN cc_start: 0.8999 (pm20) cc_final: 0.8289 (mp10) REVERT: C 19 MET cc_start: 0.8461 (tmm) cc_final: 0.7882 (tmm) REVERT: C 143 MET cc_start: 0.9167 (mpp) cc_final: 0.8924 (mpp) REVERT: C 179 LEU cc_start: 0.9605 (mm) cc_final: 0.9251 (tp) REVERT: C 198 LEU cc_start: 0.9220 (mt) cc_final: 0.8685 (pp) REVERT: C 203 GLN cc_start: 0.8955 (pm20) cc_final: 0.8200 (mp10) REVERT: D 19 MET cc_start: 0.8375 (tmm) cc_final: 0.7903 (tmm) REVERT: D 34 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.6737 (m) REVERT: D 36 ASP cc_start: 0.9021 (m-30) cc_final: 0.8665 (p0) REVERT: D 59 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8084 (mtp) REVERT: D 76 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9021 (tm-30) REVERT: D 77 GLU cc_start: 0.9092 (tt0) cc_final: 0.8590 (tm-30) REVERT: D 79 GLU cc_start: 0.9245 (pp20) cc_final: 0.8770 (pp20) REVERT: D 124 TRP cc_start: 0.9413 (m-10) cc_final: 0.8553 (m-10) REVERT: D 154 GLU cc_start: 0.9068 (pm20) cc_final: 0.8866 (pm20) REVERT: D 167 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7619 (mm-30) REVERT: D 202 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8404 (m) REVERT: D 203 GLN cc_start: 0.9056 (pm20) cc_final: 0.8760 (mp10) REVERT: E 35 GLU cc_start: 0.8826 (pm20) cc_final: 0.8498 (pm20) REVERT: E 198 LEU cc_start: 0.9008 (mt) cc_final: 0.8706 (pp) REVERT: E 203 GLN cc_start: 0.8977 (pm20) cc_final: 0.8575 (mp10) REVERT: F 19 MET cc_start: 0.8458 (tmm) cc_final: 0.8237 (tmm) REVERT: F 143 MET cc_start: 0.9161 (mpp) cc_final: 0.8917 (mpp) REVERT: F 179 LEU cc_start: 0.9611 (mm) cc_final: 0.9231 (tp) REVERT: F 203 GLN cc_start: 0.8988 (pm20) cc_final: 0.8092 (mp10) REVERT: F 210 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8770 (mmtm) outliers start: 24 outliers final: 18 residues processed: 276 average time/residue: 0.5007 time to fit residues: 149.2656 Evaluate side-chains 282 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN D 212 GLN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.082451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054472 restraints weight = 32117.458| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.60 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10218 Z= 0.178 Angle : 0.999 15.230 13836 Z= 0.479 Chirality : 0.049 0.445 1518 Planarity : 0.005 0.057 1842 Dihedral : 4.354 20.306 1386 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.08 % Allowed : 34.56 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1272 helix: 0.90 (0.18), residues: 846 sheet: -0.41 (0.49), residues: 54 loop : -0.32 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 201 TYR 0.019 0.002 TYR A 153 PHE 0.009 0.002 PHE D 37 TRP 0.032 0.003 TRP B 124 HIS 0.002 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00394 (10212) covalent geometry : angle 0.99941 (13824) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.08019 ( 12) hydrogen bonds : bond 0.04891 ( 636) hydrogen bonds : angle 5.20577 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 285 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8362 (tmm) cc_final: 0.7888 (tmm) REVERT: A 28 MET cc_start: 0.9345 (tpp) cc_final: 0.9124 (tpt) REVERT: A 76 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9019 (tm-30) REVERT: A 77 GLU cc_start: 0.9051 (tt0) cc_final: 0.8544 (tm-30) REVERT: A 79 GLU cc_start: 0.9251 (pp20) cc_final: 0.8779 (pp20) REVERT: A 120 ILE cc_start: 0.9315 (mm) cc_final: 0.9076 (mm) REVERT: A 124 TRP cc_start: 0.9344 (m-10) cc_final: 0.8889 (m-10) REVERT: A 167 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 202 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8392 (m) REVERT: A 203 GLN cc_start: 0.9049 (pm20) cc_final: 0.8770 (mp10) REVERT: B 35 GLU cc_start: 0.8670 (mp0) cc_final: 0.8281 (mp0) REVERT: B 59 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8182 (mtp) REVERT: B 179 LEU cc_start: 0.9561 (mm) cc_final: 0.9301 (tt) REVERT: B 198 LEU cc_start: 0.9256 (mt) cc_final: 0.8685 (pp) REVERT: B 203 GLN cc_start: 0.9016 (pm20) cc_final: 0.8322 (mp10) REVERT: C 19 MET cc_start: 0.8439 (tmm) cc_final: 0.8099 (tmm) REVERT: C 68 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8976 (tm-30) REVERT: C 143 MET cc_start: 0.9178 (mpp) cc_final: 0.8933 (mpp) REVERT: C 167 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7560 (mm-30) REVERT: C 179 LEU cc_start: 0.9608 (mm) cc_final: 0.9244 (tp) REVERT: C 198 LEU cc_start: 0.9231 (mt) cc_final: 0.8912 (pp) REVERT: C 203 GLN cc_start: 0.9003 (pm20) cc_final: 0.8151 (mp10) REVERT: C 209 GLU cc_start: 0.9030 (mp0) cc_final: 0.8808 (mp0) REVERT: C 210 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8582 (mptp) REVERT: D 19 MET cc_start: 0.8371 (tmm) cc_final: 0.7893 (tmm) REVERT: D 34 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.6734 (m) REVERT: D 36 ASP cc_start: 0.9017 (m-30) cc_final: 0.8694 (p0) REVERT: D 76 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9031 (tm-30) REVERT: D 77 GLU cc_start: 0.9096 (tt0) cc_final: 0.8511 (tm-30) REVERT: D 79 GLU cc_start: 0.9249 (pp20) cc_final: 0.8778 (pp20) REVERT: D 124 TRP cc_start: 0.9353 (m-10) cc_final: 0.8897 (m-10) REVERT: D 167 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7637 (mm-30) REVERT: D 202 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8396 (m) REVERT: D 203 GLN cc_start: 0.9056 (pm20) cc_final: 0.8774 (mp10) REVERT: E 35 GLU cc_start: 0.8822 (pm20) cc_final: 0.8491 (pm20) REVERT: E 179 LEU cc_start: 0.9553 (mm) cc_final: 0.9290 (tt) REVERT: E 198 LEU cc_start: 0.9023 (mt) cc_final: 0.8723 (pp) REVERT: E 203 GLN cc_start: 0.8981 (pm20) cc_final: 0.8267 (mp10) REVERT: F 19 MET cc_start: 0.8435 (tmm) cc_final: 0.8099 (tmm) REVERT: F 143 MET cc_start: 0.9171 (mpp) cc_final: 0.8924 (mpp) REVERT: F 179 LEU cc_start: 0.9610 (mm) cc_final: 0.9239 (tp) REVERT: F 203 GLN cc_start: 0.9004 (pm20) cc_final: 0.8101 (mp10) REVERT: F 210 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8770 (mmtm) outliers start: 22 outliers final: 16 residues processed: 290 average time/residue: 0.5039 time to fit residues: 157.1724 Evaluate side-chains 287 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.082125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054325 restraints weight = 32403.362| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.61 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10218 Z= 0.192 Angle : 0.984 14.623 13836 Z= 0.481 Chirality : 0.051 0.430 1518 Planarity : 0.005 0.056 1842 Dihedral : 4.309 21.823 1386 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.27 % Allowed : 34.09 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1272 helix: 0.79 (0.18), residues: 852 sheet: -0.49 (0.51), residues: 54 loop : -0.25 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 201 TYR 0.020 0.002 TYR B 176 PHE 0.009 0.002 PHE C 156 TRP 0.029 0.003 TRP C 124 HIS 0.002 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00435 (10212) covalent geometry : angle 0.98453 (13824) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.10466 ( 12) hydrogen bonds : bond 0.04937 ( 636) hydrogen bonds : angle 5.26460 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4052.77 seconds wall clock time: 69 minutes 48.41 seconds (4188.41 seconds total)