Starting phenix.real_space_refine on Tue Mar 3 23:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6o_21560/03_2026/6w6o_21560_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6o_21560/03_2026/6w6o_21560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w6o_21560/03_2026/6w6o_21560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6o_21560/03_2026/6w6o_21560.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6o_21560/03_2026/6w6o_21560_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6o_21560/03_2026/6w6o_21560_neut.cif" } resolution = 3.2 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 48 5.16 5 C 6244 2.51 5 N 1388 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9180 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "E" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "F" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "G" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "I" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.04, per 1000 atoms: 0.22 Number of scatterers: 9180 At special positions: 0 Unit cell: (150.39, 150.39, 69.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 12 15.00 O 1488 8.00 N 1388 7.00 C 6244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 17 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 24 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 17 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 24 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 17 " distance=2.03 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 24 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 31 " distance=2.03 Simple disulfide: pdb=" SG CYS I 2 " - pdb=" SG CYS I 17 " distance=2.03 Simple disulfide: pdb=" SG CYS I 9 " - pdb=" SG CYS I 24 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 31 " 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: 0.76 Conformation dependent library (CDL) restraints added in 288.5 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 66.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 Processing helix chain 'A' and resid 45 through 78 removed outlier: 3.609A pdb=" N ASP A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TRP A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.874A pdb=" N GLU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.678A pdb=" N SER A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 148 removed outlier: 3.648A pdb=" N ALA A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Proline residue: A 145 - end of helix Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.766A pdb=" N THR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 236 removed outlier: 3.628A pdb=" N PHE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 43 Processing helix chain 'D' and resid 45 through 78 removed outlier: 3.609A pdb=" N ASP D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TRP D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 106 removed outlier: 3.874A pdb=" N GLU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 Processing helix chain 'D' and resid 124 through 130 removed outlier: 3.678A pdb=" N SER D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.648A pdb=" N ALA D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.766A pdb=" N THR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 192 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 236 removed outlier: 3.627A pdb=" N PHE D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 43 Processing helix chain 'F' and resid 45 through 78 removed outlier: 3.609A pdb=" N ASP F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TRP F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER F 78 " --> pdb=" O ARG F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 106 removed outlier: 3.875A pdb=" N GLU F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 122 Processing helix chain 'F' and resid 124 through 130 removed outlier: 3.678A pdb=" N SER F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.647A pdb=" N ALA F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Proline residue: F 145 - end of helix Processing helix chain 'F' and resid 148 through 170 Processing helix chain 'F' and resid 181 through 192 removed outlier: 3.765A pdb=" N THR F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 192 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 211 through 236 removed outlier: 3.628A pdb=" N PHE F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 43 Processing helix chain 'H' and resid 45 through 78 removed outlier: 3.609A pdb=" N ASP H 51 " --> pdb=" O ARG H 47 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS H 52 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TRP H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER H 78 " --> pdb=" O ARG H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 106 removed outlier: 3.874A pdb=" N GLU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 124 through 130 removed outlier: 3.679A pdb=" N SER H 128 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 removed outlier: 3.648A pdb=" N ALA H 139 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Proline residue: H 145 - end of helix Processing helix chain 'H' and resid 148 through 170 Processing helix chain 'H' and resid 181 through 192 removed outlier: 3.766A pdb=" N THR H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR H 192 " --> pdb=" O PHE H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'H' and resid 211 through 236 removed outlier: 3.627A pdb=" N PHE H 215 " --> pdb=" O SER H 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS C 32 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 22 through 24 removed outlier: 4.136A pdb=" N LYS E 32 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS G 32 " --> pdb=" O VAL G 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS I 32 " --> pdb=" O VAL I 23 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1392 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: 1.24 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1268 1.30 - 1.42: 2532 1.42 - 1.55: 5466 1.55 - 1.68: 54 1.68 - 1.81: 72 Bond restraints: 9392 Sorted by residual: bond pdb=" C31 POV H 303 " pdb=" O31 POV H 303 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 POV A 302 " pdb=" O31 POV A 302 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C31 POV D 302 " pdb=" O31 POV D 302 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C31 POV F 303 " pdb=" O31 POV F 303 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C21 POV F 303 " pdb=" O21 POV F 303 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 9387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 11849 2.31 - 4.63: 551 4.63 - 6.94: 162 6.94 - 9.25: 46 9.25 - 11.57: 36 Bond angle restraints: 12644 Sorted by residual: angle pdb=" N SER D 82 " pdb=" CA SER D 82 " pdb=" CB SER D 82 " ideal model delta sigma weight residual 110.44 116.24 -5.80 1.43e+00 4.89e-01 1.64e+01 angle pdb=" N SER A 82 " pdb=" CA SER A 82 " pdb=" CB SER A 82 " ideal model delta sigma weight residual 110.44 116.21 -5.77 1.43e+00 4.89e-01 1.63e+01 angle pdb=" N SER F 82 " pdb=" CA SER F 82 " pdb=" CB SER F 82 " ideal model delta sigma weight residual 110.44 116.18 -5.74 1.43e+00 4.89e-01 1.61e+01 angle pdb=" N SER H 82 " pdb=" CA SER H 82 " pdb=" CB SER H 82 " ideal model delta sigma weight residual 110.44 116.16 -5.72 1.43e+00 4.89e-01 1.60e+01 angle pdb=" O11 POV H 301 " pdb=" P POV H 301 " pdb=" O12 POV H 301 " ideal model delta sigma weight residual 97.67 109.24 -11.57 3.00e+00 1.11e-01 1.49e+01 ... (remaining 12639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.75: 4942 28.75 - 57.49: 575 57.49 - 86.24: 131 86.24 - 114.98: 8 114.98 - 143.73: 12 Dihedral angle restraints: 5668 sinusoidal: 2580 harmonic: 3088 Sorted by residual: dihedral pdb=" CB CYS G 16 " pdb=" SG CYS G 16 " pdb=" SG CYS G 31 " pdb=" CB CYS G 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.02 69.02 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS E 16 " pdb=" SG CYS E 16 " pdb=" SG CYS E 31 " pdb=" CB CYS E 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.01 69.01 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS C 16 " pdb=" SG CYS C 16 " pdb=" SG CYS C 31 " pdb=" CB CYS C 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.01 69.01 1 1.00e+01 1.00e-02 6.16e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1019 0.048 - 0.097: 296 0.097 - 0.145: 73 0.145 - 0.193: 16 0.193 - 0.242: 20 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA TRP I 30 " pdb=" N TRP I 30 " pdb=" C TRP I 30 " pdb=" CB TRP I 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA TRP C 30 " pdb=" N TRP C 30 " pdb=" C TRP C 30 " pdb=" CB TRP C 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA TRP G 30 " pdb=" N TRP G 30 " pdb=" C TRP G 30 " pdb=" CB TRP G 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1421 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 81 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C LYS H 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS H 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER H 82 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 81 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C LYS F 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS F 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER F 82 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 81 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C LYS A 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS A 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 82 " -0.014 2.00e-02 2.50e+03 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 295 2.64 - 3.21: 9232 3.21 - 3.77: 13995 3.77 - 4.34: 18286 4.34 - 4.90: 30138 Nonbonded interactions: 71946 Sorted by model distance: nonbonded pdb=" O GLN E 15 " pdb=" NE2 GLN E 15 " model vdw 2.078 3.120 nonbonded pdb=" O GLN C 15 " pdb=" NE2 GLN C 15 " model vdw 2.078 3.120 nonbonded pdb=" O GLN G 15 " pdb=" NE2 GLN G 15 " model vdw 2.078 3.120 nonbonded pdb=" O GLN I 15 " pdb=" NE2 GLN I 15 " model vdw 2.079 3.120 nonbonded pdb=" N ASN G 13 " pdb=" OD1 ASN G 13 " model vdw 2.172 3.120 ... (remaining 71941 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.910 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.011 0.129 9404 Z= 0.521 Angle : 1.336 11.566 12668 Z= 0.606 Chirality : 0.055 0.242 1424 Planarity : 0.005 0.039 1464 Dihedral : 24.615 143.728 3608 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 53.37 Ramachandran Plot: Outliers : 1.56 % Allowed : 15.18 % Favored : 83.27 % Rotamer: Outliers : 16.39 % Allowed : 24.37 % Favored : 59.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.21), residues: 1028 helix: -2.38 (0.17), residues: 652 sheet: -4.67 (0.67), residues: 40 loop : -4.53 (0.22), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 202 TYR 0.010 0.002 TYR D 57 PHE 0.012 0.001 PHE A 215 TRP 0.015 0.002 TRP I 30 HIS 0.002 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.01078 ( 9392) covalent geometry : angle 1.33609 (12644) SS BOND : bond 0.00123 ( 12) SS BOND : angle 1.37695 ( 24) hydrogen bonds : bond 0.15946 ( 464) hydrogen bonds : angle 8.12793 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 229 time to evaluate : 0.219 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: A 184 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9118 (tt) REVERT: D 184 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9136 (tt) REVERT: F 184 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9125 (tt) REVERT: H 184 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9141 (tt) outliers start: 156 outliers final: 103 residues processed: 371 average time/residue: 0.0898 time to fit residues: 46.1008 Evaluate side-chains 325 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 218 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 24 CYS Chi-restraints excluded: chain E residue 34 GLN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 24 CYS Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 234 ILE Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 24 CYS Chi-restraints excluded: chain I residue 35 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN A 179 ASN A 237 ASN C 10 ASN C 15 GLN C 34 GLN ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 179 ASN D 237 ASN E 10 ASN E 15 GLN E 34 GLN ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN F 179 ASN F 237 ASN G 10 ASN G 15 GLN ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 179 ASN H 237 ASN I 10 ASN I 15 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.158125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106943 restraints weight = 13366.635| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.08 r_work: 0.3164 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9404 Z= 0.156 Angle : 0.681 7.538 12668 Z= 0.350 Chirality : 0.045 0.176 1424 Planarity : 0.004 0.028 1464 Dihedral : 22.770 145.690 1847 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 9.24 % Allowed : 21.74 % Favored : 69.01 % 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: -1.66 (0.26), residues: 1028 helix: -0.20 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.82 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 125 TYR 0.007 0.001 TYR F 214 PHE 0.014 0.001 PHE A 227 TRP 0.014 0.002 TRP C 30 HIS 0.004 0.001 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9392) covalent geometry : angle 0.67562 (12644) SS BOND : bond 0.00596 ( 12) SS BOND : angle 2.14184 ( 24) hydrogen bonds : bond 0.03808 ( 464) hydrogen bonds : angle 4.91718 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 247 time to evaluate : 0.322 Fit side-chains REVERT: A 110 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.5695 (pp20) REVERT: A 227 PHE cc_start: 0.8077 (t80) cc_final: 0.7666 (m-10) REVERT: C 7 LYS cc_start: 0.6766 (mmtp) cc_final: 0.6332 (mmtm) REVERT: D 110 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5769 (pp20) REVERT: E 7 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6860 (mmtm) REVERT: F 110 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5739 (pp20) REVERT: G 7 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6846 (mmtm) REVERT: H 110 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.5752 (pp20) REVERT: I 7 LYS cc_start: 0.6690 (mmtp) cc_final: 0.6258 (mmtm) outliers start: 88 outliers final: 44 residues processed: 325 average time/residue: 0.0864 time to fit residues: 39.3709 Evaluate side-chains 276 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 234 ILE Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN C 10 ASN C 34 GLN ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN E 34 GLN F 22 HIS G 10 ASN ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107399 restraints weight = 13375.133| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.12 r_work: 0.3166 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9404 Z= 0.146 Angle : 0.637 9.156 12668 Z= 0.322 Chirality : 0.042 0.195 1424 Planarity : 0.003 0.023 1464 Dihedral : 20.829 96.747 1717 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 9.03 % Allowed : 23.63 % Favored : 67.33 % 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: -0.47 (0.27), residues: 1028 helix: 0.74 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -2.41 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 125 TYR 0.007 0.001 TYR H 57 PHE 0.014 0.001 PHE H 230 TRP 0.013 0.001 TRP G 30 HIS 0.001 0.000 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9392) covalent geometry : angle 0.62747 (12644) SS BOND : bond 0.00482 ( 12) SS BOND : angle 2.62523 ( 24) hydrogen bonds : bond 0.03669 ( 464) hydrogen bonds : angle 4.59661 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 245 time to evaluate : 0.400 Fit side-chains REVERT: A 20 VAL cc_start: 0.6610 (OUTLIER) cc_final: 0.6378 (t) REVERT: A 27 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: A 100 SER cc_start: 0.8001 (m) cc_final: 0.7798 (m) REVERT: A 110 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.5946 (pp20) REVERT: A 227 PHE cc_start: 0.8010 (t80) cc_final: 0.7553 (m-10) REVERT: A 228 ASN cc_start: 0.8726 (m-40) cc_final: 0.8474 (m110) REVERT: C 7 LYS cc_start: 0.6841 (mmtp) cc_final: 0.6577 (mmtm) REVERT: C 17 CYS cc_start: 0.5861 (t) cc_final: 0.5493 (m) REVERT: D 20 VAL cc_start: 0.6578 (OUTLIER) cc_final: 0.6347 (t) REVERT: D 27 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: D 100 SER cc_start: 0.8096 (m) cc_final: 0.7863 (m) REVERT: D 110 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5972 (pp20) REVERT: E 7 LYS cc_start: 0.7038 (mmtt) cc_final: 0.6825 (mmtm) REVERT: E 17 CYS cc_start: 0.5715 (t) cc_final: 0.5498 (m) REVERT: F 20 VAL cc_start: 0.6580 (OUTLIER) cc_final: 0.6351 (t) REVERT: F 27 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: F 100 SER cc_start: 0.8114 (m) cc_final: 0.7897 (m) REVERT: F 110 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5859 (pp20) REVERT: H 20 VAL cc_start: 0.6814 (OUTLIER) cc_final: 0.6590 (t) REVERT: H 27 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: H 100 SER cc_start: 0.8095 (m) cc_final: 0.7890 (m) REVERT: H 110 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5933 (pp20) outliers start: 86 outliers final: 38 residues processed: 315 average time/residue: 0.0819 time to fit residues: 36.7817 Evaluate side-chains 289 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 239 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 36 ASN C 10 ASN C 15 GLN C 34 GLN D 22 HIS D 36 ASN D 149 ASN D 228 ASN E 10 ASN E 15 GLN E 34 GLN F 36 ASN F 149 ASN G 10 ASN H 22 HIS H 36 ASN H 149 ASN H 228 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.160080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107788 restraints weight = 13313.577| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.13 r_work: 0.3163 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9404 Z= 0.138 Angle : 0.617 8.768 12668 Z= 0.306 Chirality : 0.041 0.173 1424 Planarity : 0.003 0.022 1464 Dihedral : 20.466 89.331 1707 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 8.72 % Allowed : 24.89 % Favored : 66.39 % 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: -0.01 (0.27), residues: 1028 helix: 1.00 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -2.19 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 125 TYR 0.008 0.001 TYR H 57 PHE 0.010 0.001 PHE F 205 TRP 0.012 0.001 TRP G 30 HIS 0.001 0.000 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9392) covalent geometry : angle 0.61336 (12644) SS BOND : bond 0.00281 ( 12) SS BOND : angle 1.72631 ( 24) hydrogen bonds : bond 0.03522 ( 464) hydrogen bonds : angle 4.53104 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 0.321 Fit side-chains REVERT: A 20 VAL cc_start: 0.6776 (OUTLIER) cc_final: 0.6556 (t) REVERT: A 27 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: A 90 ASN cc_start: 0.8807 (m-40) cc_final: 0.8479 (m110) REVERT: A 110 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5982 (pp20) REVERT: A 227 PHE cc_start: 0.7931 (t80) cc_final: 0.7505 (m-80) REVERT: A 228 ASN cc_start: 0.8832 (m110) cc_final: 0.8295 (m110) REVERT: C 34 GLN cc_start: 0.6929 (tt0) cc_final: 0.6695 (tt0) REVERT: D 20 VAL cc_start: 0.6774 (OUTLIER) cc_final: 0.6553 (t) REVERT: D 27 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: D 100 SER cc_start: 0.8069 (m) cc_final: 0.7863 (m) REVERT: D 110 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.5999 (pp20) REVERT: D 228 ASN cc_start: 0.8515 (m-40) cc_final: 0.8296 (m110) REVERT: E 34 GLN cc_start: 0.6810 (tt0) cc_final: 0.6607 (tt0) REVERT: F 20 VAL cc_start: 0.6679 (OUTLIER) cc_final: 0.6455 (t) REVERT: F 27 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: F 90 ASN cc_start: 0.8772 (m-40) cc_final: 0.8432 (m110) REVERT: F 110 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5776 (pp20) REVERT: F 228 ASN cc_start: 0.8649 (m110) cc_final: 0.8290 (m110) REVERT: G 34 GLN cc_start: 0.5931 (pm20) cc_final: 0.5718 (pm20) REVERT: H 20 VAL cc_start: 0.6768 (OUTLIER) cc_final: 0.6560 (t) REVERT: H 27 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: H 90 ASN cc_start: 0.8766 (m-40) cc_final: 0.8431 (m110) REVERT: H 100 SER cc_start: 0.7985 (m) cc_final: 0.7774 (m) REVERT: H 110 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5847 (pp20) REVERT: H 228 ASN cc_start: 0.8534 (m-40) cc_final: 0.8286 (m110) outliers start: 83 outliers final: 43 residues processed: 324 average time/residue: 0.0806 time to fit residues: 37.5499 Evaluate side-chains 297 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 88 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN E 10 ASN G 10 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.161150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108801 restraints weight = 13236.468| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.14 r_work: 0.3180 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9404 Z= 0.128 Angle : 0.637 9.066 12668 Z= 0.311 Chirality : 0.041 0.152 1424 Planarity : 0.003 0.022 1464 Dihedral : 19.633 94.036 1701 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 8.09 % Allowed : 28.05 % Favored : 63.87 % 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: 0.15 (0.27), residues: 1028 helix: 1.22 (0.20), residues: 692 sheet: -3.80 (0.65), residues: 48 loop : -1.93 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 125 TYR 0.015 0.001 TYR A 57 PHE 0.022 0.001 PHE H 105 TRP 0.011 0.001 TRP G 30 HIS 0.001 0.000 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9392) covalent geometry : angle 0.62987 (12644) SS BOND : bond 0.00399 ( 12) SS BOND : angle 2.28619 ( 24) hydrogen bonds : bond 0.03493 ( 464) hydrogen bonds : angle 4.48314 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 257 time to evaluate : 0.353 Fit side-chains REVERT: A 27 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: A 90 ASN cc_start: 0.8777 (m-40) cc_final: 0.8442 (m110) REVERT: A 110 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5939 (pp20) REVERT: A 227 PHE cc_start: 0.7911 (t80) cc_final: 0.7496 (m-80) REVERT: D 20 VAL cc_start: 0.6710 (OUTLIER) cc_final: 0.6497 (t) REVERT: D 90 ASN cc_start: 0.8778 (m-40) cc_final: 0.8433 (m110) REVERT: D 100 SER cc_start: 0.7992 (m) cc_final: 0.7784 (m) REVERT: D 110 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5930 (pp20) REVERT: D 228 ASN cc_start: 0.8549 (m-40) cc_final: 0.8347 (m110) REVERT: F 20 VAL cc_start: 0.6616 (OUTLIER) cc_final: 0.6399 (t) REVERT: F 27 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: F 90 ASN cc_start: 0.8794 (m-40) cc_final: 0.8441 (m110) REVERT: F 110 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5564 (pp20) REVERT: F 134 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7264 (ttp-110) REVERT: F 228 ASN cc_start: 0.8641 (m110) cc_final: 0.8298 (m110) REVERT: G 34 GLN cc_start: 0.6038 (pm20) cc_final: 0.5823 (pm20) REVERT: H 27 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: H 90 ASN cc_start: 0.8758 (m-40) cc_final: 0.8422 (m110) REVERT: H 100 SER cc_start: 0.7947 (m) cc_final: 0.7745 (m) REVERT: H 110 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5607 (pp20) REVERT: H 228 ASN cc_start: 0.8442 (m-40) cc_final: 0.8208 (m110) outliers start: 77 outliers final: 47 residues processed: 310 average time/residue: 0.0799 time to fit residues: 35.5189 Evaluate side-chains 303 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 167 MET Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 0.0050 chunk 96 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN C 34 GLN D 36 ASN E 10 ASN F 36 ASN G 10 ASN H 36 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.162712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111069 restraints weight = 13198.985| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.11 r_work: 0.3208 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9404 Z= 0.117 Angle : 0.621 8.830 12668 Z= 0.301 Chirality : 0.040 0.135 1424 Planarity : 0.003 0.021 1464 Dihedral : 18.827 98.109 1701 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.20 % Allowed : 31.62 % Favored : 62.18 % 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 (0.27), residues: 1028 helix: 1.43 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.03 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 202 TYR 0.018 0.001 TYR A 57 PHE 0.020 0.001 PHE H 105 TRP 0.012 0.001 TRP I 30 HIS 0.001 0.000 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9392) covalent geometry : angle 0.61609 (12644) SS BOND : bond 0.00489 ( 12) SS BOND : angle 1.93886 ( 24) hydrogen bonds : bond 0.03288 ( 464) hydrogen bonds : angle 4.41124 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 0.277 Fit side-chains REVERT: A 27 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: A 81 LYS cc_start: 0.4678 (OUTLIER) cc_final: 0.4091 (tppt) REVERT: A 90 ASN cc_start: 0.8767 (m-40) cc_final: 0.8424 (m-40) REVERT: A 110 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5962 (pp20) REVERT: A 202 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8644 (mmt180) REVERT: A 227 PHE cc_start: 0.7794 (t80) cc_final: 0.7393 (m-80) REVERT: A 228 ASN cc_start: 0.8592 (m-40) cc_final: 0.8105 (m110) REVERT: C 34 GLN cc_start: 0.6944 (tt0) cc_final: 0.6585 (pm20) REVERT: D 20 VAL cc_start: 0.6662 (OUTLIER) cc_final: 0.6452 (t) REVERT: D 65 TRP cc_start: 0.7658 (OUTLIER) cc_final: 0.6904 (t-100) REVERT: D 81 LYS cc_start: 0.4650 (OUTLIER) cc_final: 0.4091 (tppt) REVERT: D 90 ASN cc_start: 0.8760 (m-40) cc_final: 0.8399 (m-40) REVERT: D 100 SER cc_start: 0.7978 (m) cc_final: 0.7478 (p) REVERT: D 110 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: D 202 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8643 (mmt180) REVERT: D 228 ASN cc_start: 0.8511 (m-40) cc_final: 0.8231 (m110) REVERT: E 34 GLN cc_start: 0.6841 (tt0) cc_final: 0.6545 (pm20) REVERT: F 65 TRP cc_start: 0.7602 (OUTLIER) cc_final: 0.6905 (t-100) REVERT: F 81 LYS cc_start: 0.4711 (OUTLIER) cc_final: 0.4129 (tppt) REVERT: F 90 ASN cc_start: 0.8781 (m-40) cc_final: 0.8422 (m110) REVERT: F 110 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5513 (pp20) REVERT: F 228 ASN cc_start: 0.8582 (m110) cc_final: 0.8169 (m110) REVERT: G 34 GLN cc_start: 0.5832 (pm20) cc_final: 0.5608 (pm20) REVERT: H 27 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: H 65 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.6927 (t-100) REVERT: H 81 LYS cc_start: 0.4754 (OUTLIER) cc_final: 0.4210 (tppt) REVERT: H 90 ASN cc_start: 0.8755 (m-40) cc_final: 0.8409 (m110) REVERT: H 100 SER cc_start: 0.7930 (m) cc_final: 0.7466 (p) REVERT: H 110 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5470 (pp20) REVERT: H 228 ASN cc_start: 0.8416 (m-40) cc_final: 0.8194 (m110) outliers start: 59 outliers final: 32 residues processed: 297 average time/residue: 0.0841 time to fit residues: 35.1440 Evaluate side-chains 288 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 167 MET Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 93 optimal weight: 0.0770 chunk 99 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN E 10 ASN G 10 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106337 restraints weight = 13169.747| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.09 r_work: 0.3139 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9404 Z= 0.187 Angle : 0.681 9.272 12668 Z= 0.332 Chirality : 0.042 0.122 1424 Planarity : 0.003 0.022 1464 Dihedral : 19.811 103.352 1688 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.88 % Allowed : 31.93 % Favored : 62.18 % 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: 0.58 (0.27), residues: 1028 helix: 1.30 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.60 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 29 TYR 0.023 0.002 TYR F 57 PHE 0.024 0.002 PHE F 105 TRP 0.011 0.001 TRP C 30 HIS 0.001 0.001 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9392) covalent geometry : angle 0.67723 (12644) SS BOND : bond 0.00241 ( 12) SS BOND : angle 1.83313 ( 24) hydrogen bonds : bond 0.03807 ( 464) hydrogen bonds : angle 4.56312 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.273 Fit side-chains REVERT: A 27 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: A 90 ASN cc_start: 0.8811 (m-40) cc_final: 0.8513 (m110) REVERT: A 110 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6069 (pp20) REVERT: A 227 PHE cc_start: 0.7868 (t80) cc_final: 0.7417 (m-10) REVERT: A 228 ASN cc_start: 0.8692 (m-40) cc_final: 0.8290 (m110) REVERT: C 34 GLN cc_start: 0.6880 (tt0) cc_final: 0.6648 (pm20) REVERT: D 90 ASN cc_start: 0.8781 (m-40) cc_final: 0.8454 (m110) REVERT: D 110 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6049 (pp20) REVERT: D 237 ASN cc_start: 0.7958 (m110) cc_final: 0.7743 (m110) REVERT: E 34 GLN cc_start: 0.6685 (tt0) cc_final: 0.6312 (pm20) REVERT: F 27 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: F 90 ASN cc_start: 0.8767 (m-40) cc_final: 0.8454 (m110) REVERT: F 110 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5741 (pp20) REVERT: G 34 GLN cc_start: 0.5769 (pm20) cc_final: 0.5563 (pm20) REVERT: H 27 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: H 90 ASN cc_start: 0.8781 (m-40) cc_final: 0.8489 (m110) REVERT: H 110 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5733 (pp20) REVERT: H 228 ASN cc_start: 0.8464 (m-40) cc_final: 0.8238 (m110) outliers start: 56 outliers final: 33 residues processed: 275 average time/residue: 0.0817 time to fit residues: 31.9414 Evaluate side-chains 260 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 81 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN D 228 ASN E 10 ASN F 36 ASN G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.161528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109459 restraints weight = 13187.865| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.10 r_work: 0.3186 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9404 Z= 0.133 Angle : 0.657 8.908 12668 Z= 0.319 Chirality : 0.041 0.127 1424 Planarity : 0.003 0.020 1464 Dihedral : 18.929 110.049 1688 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.88 % Allowed : 31.51 % Favored : 62.61 % 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: 0.63 (0.27), residues: 1028 helix: 1.40 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 29 TYR 0.015 0.001 TYR F 57 PHE 0.023 0.001 PHE F 105 TRP 0.013 0.001 TRP C 30 HIS 0.002 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9392) covalent geometry : angle 0.65319 (12644) SS BOND : bond 0.00205 ( 12) SS BOND : angle 1.79228 ( 24) hydrogen bonds : bond 0.03535 ( 464) hydrogen bonds : angle 4.47089 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.325 Fit side-chains REVERT: A 27 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: A 90 ASN cc_start: 0.8749 (m-40) cc_final: 0.8428 (m110) REVERT: A 110 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6043 (pp20) REVERT: A 227 PHE cc_start: 0.7853 (t80) cc_final: 0.7506 (m-10) REVERT: A 228 ASN cc_start: 0.8599 (m-40) cc_final: 0.8155 (m110) REVERT: C 34 GLN cc_start: 0.6879 (tt0) cc_final: 0.6650 (pm20) REVERT: D 65 TRP cc_start: 0.7585 (m-10) cc_final: 0.6909 (t-100) REVERT: D 100 SER cc_start: 0.8145 (m) cc_final: 0.7911 (m) REVERT: D 110 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6002 (pp20) REVERT: D 237 ASN cc_start: 0.8019 (m110) cc_final: 0.7783 (m110) REVERT: E 34 GLN cc_start: 0.6741 (tt0) cc_final: 0.6440 (pm20) REVERT: F 27 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: F 65 TRP cc_start: 0.7655 (OUTLIER) cc_final: 0.6947 (t-100) REVERT: F 90 ASN cc_start: 0.8758 (m-40) cc_final: 0.8419 (m110) REVERT: F 110 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5610 (pp20) REVERT: H 27 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: H 65 TRP cc_start: 0.7711 (OUTLIER) cc_final: 0.6977 (t-100) REVERT: H 90 ASN cc_start: 0.8726 (m-40) cc_final: 0.8409 (m110) REVERT: H 110 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5571 (pp20) REVERT: H 228 ASN cc_start: 0.8327 (m-40) cc_final: 0.8098 (m110) outliers start: 56 outliers final: 35 residues processed: 257 average time/residue: 0.0803 time to fit residues: 29.5601 Evaluate side-chains 260 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN E 10 ASN F 36 ASN G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112157 restraints weight = 13176.696| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.08 r_work: 0.3230 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9404 Z= 0.120 Angle : 0.646 10.361 12668 Z= 0.313 Chirality : 0.040 0.130 1424 Planarity : 0.003 0.021 1464 Dihedral : 18.099 113.480 1688 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.46 % Allowed : 30.99 % Favored : 63.55 % 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: 0.75 (0.27), residues: 1028 helix: 1.52 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.90 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 29 TYR 0.014 0.001 TYR A 57 PHE 0.021 0.001 PHE F 105 TRP 0.017 0.001 TRP G 30 HIS 0.002 0.001 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9392) covalent geometry : angle 0.64254 (12644) SS BOND : bond 0.00244 ( 12) SS BOND : angle 1.72936 ( 24) hydrogen bonds : bond 0.03362 ( 464) hydrogen bonds : angle 4.38152 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 0.359 Fit side-chains REVERT: A 27 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: A 65 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.6917 (t-100) REVERT: A 81 LYS cc_start: 0.4655 (OUTLIER) cc_final: 0.4096 (tppt) REVERT: A 110 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5883 (pp20) REVERT: A 202 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8652 (mmt180) REVERT: A 227 PHE cc_start: 0.7789 (t80) cc_final: 0.7462 (m-10) REVERT: A 228 ASN cc_start: 0.8488 (m-40) cc_final: 0.8103 (m110) REVERT: C 34 GLN cc_start: 0.6912 (tt0) cc_final: 0.6669 (pm20) REVERT: D 65 TRP cc_start: 0.7389 (m-10) cc_final: 0.6803 (t-100) REVERT: D 81 LYS cc_start: 0.4715 (OUTLIER) cc_final: 0.4170 (tppt) REVERT: D 110 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5849 (pp20) REVERT: E 34 GLN cc_start: 0.6979 (tt0) cc_final: 0.6690 (pm20) REVERT: F 27 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: F 65 TRP cc_start: 0.7499 (OUTLIER) cc_final: 0.6869 (t-100) REVERT: F 81 LYS cc_start: 0.4683 (OUTLIER) cc_final: 0.4130 (tppt) REVERT: F 110 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5398 (pp20) REVERT: H 65 TRP cc_start: 0.7577 (m-10) cc_final: 0.6872 (t-100) REVERT: H 81 LYS cc_start: 0.4688 (OUTLIER) cc_final: 0.4117 (tppt) REVERT: H 110 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5391 (pp20) REVERT: H 228 ASN cc_start: 0.8266 (m-40) cc_final: 0.8041 (m110) outliers start: 52 outliers final: 28 residues processed: 271 average time/residue: 0.0801 time to fit residues: 31.2748 Evaluate side-chains 256 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN E 10 ASN F 36 ASN F 228 ASN G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111574 restraints weight = 13198.520| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.05 r_work: 0.3221 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9404 Z= 0.126 Angle : 0.673 10.716 12668 Z= 0.322 Chirality : 0.041 0.187 1424 Planarity : 0.003 0.026 1464 Dihedral : 17.796 113.878 1680 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.04 % Allowed : 32.88 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.27), residues: 1028 helix: 1.54 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -1.77 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 29 TYR 0.012 0.001 TYR A 57 PHE 0.021 0.001 PHE F 105 TRP 0.029 0.001 TRP H 196 HIS 0.002 0.001 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9392) covalent geometry : angle 0.66984 (12644) SS BOND : bond 0.00196 ( 12) SS BOND : angle 1.67416 ( 24) hydrogen bonds : bond 0.03439 ( 464) hydrogen bonds : angle 4.41629 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.259 Fit side-chains REVERT: A 65 TRP cc_start: 0.7512 (m-10) cc_final: 0.6906 (t-100) REVERT: A 81 LYS cc_start: 0.4523 (OUTLIER) cc_final: 0.3975 (tppt) REVERT: A 110 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5865 (pp20) REVERT: A 227 PHE cc_start: 0.7792 (t80) cc_final: 0.7464 (m-10) REVERT: A 228 ASN cc_start: 0.8486 (m-40) cc_final: 0.8091 (m110) REVERT: C 34 GLN cc_start: 0.6920 (tt0) cc_final: 0.6672 (pm20) REVERT: D 65 TRP cc_start: 0.7364 (m-10) cc_final: 0.6835 (t-100) REVERT: D 81 LYS cc_start: 0.4824 (OUTLIER) cc_final: 0.4301 (tppt) REVERT: D 110 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5819 (pp20) REVERT: E 34 GLN cc_start: 0.6938 (tt0) cc_final: 0.6626 (pm20) REVERT: F 27 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: F 65 TRP cc_start: 0.7501 (OUTLIER) cc_final: 0.6892 (t-100) REVERT: F 81 LYS cc_start: 0.4593 (OUTLIER) cc_final: 0.4117 (tppt) REVERT: F 110 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5382 (pp20) REVERT: H 65 TRP cc_start: 0.7525 (m-10) cc_final: 0.6961 (t-100) REVERT: H 81 LYS cc_start: 0.4622 (OUTLIER) cc_final: 0.4123 (tppt) REVERT: H 110 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5344 (pp20) REVERT: H 228 ASN cc_start: 0.8272 (m-40) cc_final: 0.8042 (m110) outliers start: 48 outliers final: 29 residues processed: 261 average time/residue: 0.0776 time to fit residues: 29.5152 Evaluate side-chains 250 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN E 10 ASN F 36 ASN G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.162931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110591 restraints weight = 13213.502| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.05 r_work: 0.3205 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9404 Z= 0.136 Angle : 0.692 10.763 12668 Z= 0.332 Chirality : 0.043 0.217 1424 Planarity : 0.003 0.028 1464 Dihedral : 17.768 116.598 1676 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.04 % Allowed : 32.67 % Favored : 62.29 % 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: 0.80 (0.27), residues: 1028 helix: 1.47 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -1.91 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 29 TYR 0.011 0.001 TYR A 57 PHE 0.032 0.001 PHE F 105 TRP 0.034 0.001 TRP H 196 HIS 0.002 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9392) covalent geometry : angle 0.68964 (12644) SS BOND : bond 0.00167 ( 12) SS BOND : angle 1.59700 ( 24) hydrogen bonds : bond 0.03575 ( 464) hydrogen bonds : angle 4.53058 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.31 seconds wall clock time: 42 minutes 57.75 seconds (2577.75 seconds total)