Starting phenix.real_space_refine on Mon Nov 17 23:58:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6o_21560/11_2025/6w6o_21560_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6o_21560/11_2025/6w6o_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 { model { file = "/net/cci-nas-00/data/ceres_data/6w6o_21560/11_2025/6w6o_21560_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6o_21560/11_2025/6w6o_21560_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w6o_21560/11_2025/6w6o_21560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6o_21560/11_2025/6w6o_21560.map" } 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-2.0-5881/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: 2.25, per 1000 atoms: 0.25 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: 1.02 Conformation dependent library (CDL) restraints added in 253.6 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: 0.25 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: 1.25 Time building geometry restraints manager: 1.29 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: 0.03 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: 1.170 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.400 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.500 ------------------------------------------------------------------------------- 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 : 0.440 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: 0.9119 (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: 0.9142 (tt) outliers start: 156 outliers final: 103 residues processed: 371 average time/residue: 0.0969 time to fit residues: 49.7107 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 : 0.346 ------------------------------------------------------------------------------- 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 : 0.352 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: 0.5753 (pp20) REVERT: I 7 LYS cc_start: 0.6689 (mmtp) cc_final: 0.6258 (mmtm) outliers start: 88 outliers final: 44 residues processed: 325 average time/residue: 0.0916 time to fit residues: 41.6202 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 : 0.360 ------------------------------------------------------------------------------- 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 : 0.281 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: 0.7393 (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: 0.6578 (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: 0.6581 (OUTLIER) cc_final: 0.6351 (t) REVERT: F 27 PHE cc_start: 0.8049 (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: 0.5858 (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: 0.5931 (pp20) outliers start: 86 outliers final: 38 residues processed: 315 average time/residue: 0.0867 time to fit residues: 38.8997 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 : 0.279 ------------------------------------------------------------------------------- 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 : 0.383 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: 0.6000 (pp20) REVERT: D 228 ASN cc_start: 0.8514 (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: 0.8061 (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: 0.8648 (m110) cc_final: 0.8289 (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: 0.0861 time to fit residues: 39.9897 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 : 0.367 ------------------------------------------------------------------------------- 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 : 0.269 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: 0.8443 (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: 0.7495 (m-80) REVERT: D 20 VAL cc_start: 0.6710 (OUTLIER) cc_final: 0.6497 (t) REVERT: D 90 ASN cc_start: 0.8779 (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: E 34 GLN cc_start: 0.6927 (tt0) cc_final: 0.6727 (tt0) REVERT: F 20 VAL cc_start: 0.6617 (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: 0.7381 (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: 0.8207 (m110) outliers start: 77 outliers final: 47 residues processed: 310 average time/residue: 0.0840 time to fit residues: 37.3413 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 : 0.307 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.162900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111285 restraints weight = 13225.788| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.07 r_work: 0.3217 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4341 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= 0.117 Angle : 0.621 8.835 12668 Z= 0.300 Chirality : 0.041 0.139 1424 Planarity : 0.003 0.021 1464 Dihedral : 18.837 97.962 1701 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.41 % Allowed : 31.30 % 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: 0.57 (0.27), residues: 1028 helix: 1.43 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 125 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 A 22 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9392) covalent geometry : angle 0.61543 (12644) SS BOND : bond 0.00225 ( 12) SS BOND : angle 1.95891 ( 24) hydrogen bonds : bond 0.03301 ( 464) hydrogen bonds : angle 4.40723 ( 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 318 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 257 time to evaluate : 0.367 Fit side-chains REVERT: A 27 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: A 81 LYS cc_start: 0.4684 (OUTLIER) cc_final: 0.4095 (tppt) REVERT: A 90 ASN cc_start: 0.8767 (m-40) cc_final: 0.8429 (m-40) REVERT: A 110 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5948 (pp20) REVERT: A 202 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8641 (mmt180) REVERT: A 227 PHE cc_start: 0.7775 (t80) cc_final: 0.7347 (m-80) REVERT: A 228 ASN cc_start: 0.8589 (m-40) cc_final: 0.8105 (m110) REVERT: C 34 GLN cc_start: 0.6941 (tt0) cc_final: 0.6577 (pm20) REVERT: D 20 VAL cc_start: 0.6662 (OUTLIER) cc_final: 0.6453 (t) REVERT: D 65 TRP cc_start: 0.7656 (OUTLIER) cc_final: 0.6902 (t-100) REVERT: D 81 LYS cc_start: 0.4654 (OUTLIER) cc_final: 0.4091 (tppt) REVERT: D 90 ASN cc_start: 0.8760 (m-40) cc_final: 0.8398 (m-40) REVERT: D 100 SER cc_start: 0.7977 (m) cc_final: 0.7474 (p) REVERT: D 110 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5905 (pp20) REVERT: D 202 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8639 (mmt180) REVERT: D 228 ASN cc_start: 0.8504 (m-40) cc_final: 0.8225 (m110) REVERT: F 65 TRP cc_start: 0.7662 (OUTLIER) cc_final: 0.6929 (t-100) REVERT: F 81 LYS cc_start: 0.4712 (OUTLIER) cc_final: 0.4130 (tppt) REVERT: F 90 ASN cc_start: 0.8782 (m-40) cc_final: 0.8425 (m110) REVERT: F 110 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5474 (pp20) REVERT: F 228 ASN cc_start: 0.8576 (m110) cc_final: 0.8163 (m110) REVERT: G 34 GLN cc_start: 0.5818 (pm20) cc_final: 0.5596 (pm20) REVERT: H 27 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: H 65 TRP cc_start: 0.7680 (OUTLIER) cc_final: 0.6923 (t-100) REVERT: H 81 LYS cc_start: 0.4757 (OUTLIER) cc_final: 0.4211 (tppt) REVERT: H 90 ASN cc_start: 0.8753 (m-40) cc_final: 0.8408 (m110) REVERT: H 100 SER cc_start: 0.7926 (m) cc_final: 0.7462 (p) REVERT: H 110 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5433 (pp20) REVERT: H 228 ASN cc_start: 0.8409 (m-40) cc_final: 0.8189 (m110) outliers start: 61 outliers final: 31 residues processed: 298 average time/residue: 0.0892 time to fit residues: 37.6259 Evaluate side-chains 285 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 43 optimal weight: 0.7980 chunk 93 optimal weight: 0.0370 chunk 99 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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 I 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.160874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108631 restraints weight = 13161.181| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.11 r_work: 0.3173 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9404 Z= 0.143 Angle : 0.652 9.722 12668 Z= 0.315 Chirality : 0.041 0.122 1424 Planarity : 0.003 0.021 1464 Dihedral : 19.037 102.219 1688 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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: 0.62 (0.27), residues: 1028 helix: 1.40 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 29 TYR 0.020 0.001 TYR F 57 PHE 0.024 0.001 PHE F 105 TRP 0.013 0.001 TRP C 30 HIS 0.001 0.000 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9392) covalent geometry : angle 0.64733 (12644) SS BOND : bond 0.00248 ( 12) SS BOND : angle 1.82172 ( 24) hydrogen bonds : bond 0.03508 ( 464) hydrogen bonds : angle 4.42993 ( 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 299 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 0.342 Fit side-chains REVERT: A 27 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: A 90 ASN cc_start: 0.8772 (m-40) cc_final: 0.8461 (m-40) REVERT: A 110 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6016 (pp20) REVERT: A 227 PHE cc_start: 0.7802 (t80) cc_final: 0.7413 (m-10) REVERT: A 228 ASN cc_start: 0.8625 (m-40) cc_final: 0.8154 (m110) REVERT: C 34 GLN cc_start: 0.6912 (tt0) cc_final: 0.6635 (pm20) REVERT: D 20 VAL cc_start: 0.6462 (OUTLIER) cc_final: 0.6260 (t) REVERT: D 90 ASN cc_start: 0.8763 (m-40) cc_final: 0.8439 (m110) REVERT: D 100 SER cc_start: 0.8118 (m) cc_final: 0.7907 (m) REVERT: D 110 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5994 (pp20) REVERT: D 228 ASN cc_start: 0.8556 (m-40) cc_final: 0.8286 (m110) REVERT: D 237 ASN cc_start: 0.7904 (m110) cc_final: 0.7677 (m110) REVERT: E 34 GLN cc_start: 0.6719 (tt0) cc_final: 0.6475 (pm20) REVERT: F 27 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: F 90 ASN cc_start: 0.8782 (m-40) cc_final: 0.8454 (m110) REVERT: F 110 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5652 (pp20) REVERT: F 228 ASN cc_start: 0.8624 (m110) cc_final: 0.8243 (m110) REVERT: H 27 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: H 90 ASN cc_start: 0.8748 (m-40) cc_final: 0.8444 (m110) REVERT: H 100 SER cc_start: 0.8103 (m) cc_final: 0.7903 (m) REVERT: H 110 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5593 (pp20) REVERT: H 228 ASN cc_start: 0.8346 (m-40) cc_final: 0.8118 (m110) outliers start: 56 outliers final: 41 residues processed: 281 average time/residue: 0.0875 time to fit residues: 35.0416 Evaluate side-chains 275 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 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 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 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 194 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.159436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107309 restraints weight = 13160.907| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.06 r_work: 0.3153 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9404 Z= 0.174 Angle : 0.681 8.718 12668 Z= 0.332 Chirality : 0.042 0.119 1424 Planarity : 0.003 0.022 1464 Dihedral : 19.401 109.778 1688 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.30 % Allowed : 31.93 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 1028 helix: 1.38 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.017 0.002 TYR F 57 PHE 0.022 0.001 PHE F 105 TRP 0.010 0.001 TRP F 196 HIS 0.001 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9392) covalent geometry : angle 0.67697 (12644) SS BOND : bond 0.00232 ( 12) SS BOND : angle 1.79948 ( 24) hydrogen bonds : bond 0.03729 ( 464) hydrogen bonds : angle 4.54031 ( 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 289 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 0.351 Fit side-chains REVERT: A 27 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: A 90 ASN cc_start: 0.8807 (m-40) cc_final: 0.8501 (m110) REVERT: A 110 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6093 (pp20) REVERT: A 227 PHE cc_start: 0.7862 (t80) cc_final: 0.7438 (m-10) REVERT: A 228 ASN cc_start: 0.8653 (m-40) cc_final: 0.8173 (m110) REVERT: C 34 GLN cc_start: 0.6885 (tt0) cc_final: 0.6659 (pm20) REVERT: D 90 ASN cc_start: 0.8777 (m-40) cc_final: 0.8454 (m110) REVERT: D 110 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6065 (pp20) REVERT: D 228 ASN cc_start: 0.8564 (m-40) cc_final: 0.8304 (m110) REVERT: D 237 ASN cc_start: 0.8027 (m110) cc_final: 0.7812 (m110) REVERT: E 34 GLN cc_start: 0.6748 (tt0) cc_final: 0.6506 (pm20) REVERT: F 27 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: F 90 ASN cc_start: 0.8762 (m-40) cc_final: 0.8452 (m110) REVERT: F 110 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5679 (pp20) REVERT: H 27 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: H 90 ASN cc_start: 0.8759 (m-40) cc_final: 0.8460 (m110) REVERT: H 110 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5660 (pp20) REVERT: H 228 ASN cc_start: 0.8402 (m-40) cc_final: 0.8184 (m110) outliers start: 60 outliers final: 37 residues processed: 268 average time/residue: 0.0818 time to fit residues: 31.5069 Evaluate side-chains 271 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 194 GLU 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 167 MET 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 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 194 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.161736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109534 restraints weight = 13121.219| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.11 r_work: 0.3187 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9404 Z= 0.136 Angle : 0.659 10.466 12668 Z= 0.320 Chirality : 0.041 0.127 1424 Planarity : 0.003 0.022 1464 Dihedral : 18.676 113.207 1688 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.88 % Allowed : 30.78 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.27), residues: 1028 helix: 1.45 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.80 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 29 TYR 0.018 0.001 TYR A 57 PHE 0.022 0.001 PHE F 105 TRP 0.015 0.001 TRP G 30 HIS 0.002 0.001 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9392) covalent geometry : angle 0.65564 (12644) SS BOND : bond 0.00187 ( 12) SS BOND : angle 1.75358 ( 24) hydrogen bonds : bond 0.03521 ( 464) hydrogen bonds : angle 4.46222 ( 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 287 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 0.354 Fit side-chains REVERT: A 27 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: A 90 ASN cc_start: 0.8729 (m-40) cc_final: 0.8429 (m110) REVERT: A 110 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6089 (pp20) REVERT: A 227 PHE cc_start: 0.7848 (t80) cc_final: 0.7503 (m-10) REVERT: A 228 ASN cc_start: 0.8588 (m-40) cc_final: 0.8130 (m110) REVERT: C 34 GLN cc_start: 0.6934 (tt0) cc_final: 0.6668 (pm20) REVERT: D 65 TRP cc_start: 0.7488 (OUTLIER) cc_final: 0.6862 (t-100) REVERT: D 100 SER cc_start: 0.8126 (m) cc_final: 0.7875 (m) REVERT: D 110 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6002 (pp20) REVERT: D 228 ASN cc_start: 0.8542 (m-40) cc_final: 0.8267 (m110) REVERT: E 34 GLN cc_start: 0.6858 (tt0) cc_final: 0.6553 (pm20) REVERT: F 27 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: F 65 TRP cc_start: 0.7506 (m-10) cc_final: 0.6923 (t-100) REVERT: F 110 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5579 (pp20) REVERT: H 27 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: H 65 TRP cc_start: 0.7561 (m-10) cc_final: 0.6913 (t-100) REVERT: H 90 ASN cc_start: 0.8720 (m-40) cc_final: 0.8415 (m110) REVERT: H 100 SER cc_start: 0.8136 (m) cc_final: 0.7911 (m) REVERT: H 110 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5506 (pp20) REVERT: H 228 ASN cc_start: 0.8348 (m-40) cc_final: 0.8123 (m110) outliers start: 56 outliers final: 35 residues processed: 269 average time/residue: 0.0854 time to fit residues: 32.9278 Evaluate side-chains 267 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain C residue 16 CYS 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 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 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 194 GLU Chi-restraints excluded: chain F residue 213 LEU 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 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 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: 0.0770 chunk 24 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 86 optimal weight: 0.0050 chunk 94 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.2150 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.165473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114752 restraints weight = 13292.038| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.06 r_work: 0.3272 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9404 Z= 0.116 Angle : 0.657 10.736 12668 Z= 0.313 Chirality : 0.040 0.144 1424 Planarity : 0.003 0.023 1464 Dihedral : 17.568 115.097 1680 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.15 % Allowed : 31.41 % Favored : 63.45 % 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: 0.83 (0.27), residues: 1028 helix: 1.49 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.86 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 29 TYR 0.015 0.001 TYR D 57 PHE 0.021 0.001 PHE F 105 TRP 0.015 0.001 TRP G 30 HIS 0.002 0.001 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9392) covalent geometry : angle 0.65368 (12644) SS BOND : bond 0.00150 ( 12) SS BOND : angle 1.63515 ( 24) hydrogen bonds : bond 0.03253 ( 464) hydrogen bonds : angle 4.33632 ( 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 290 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.357 Fit side-chains REVERT: A 65 TRP cc_start: 0.7443 (m-10) cc_final: 0.6814 (t-100) REVERT: A 81 LYS cc_start: 0.4600 (OUTLIER) cc_final: 0.4077 (tppt) REVERT: A 110 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5810 (pp20) REVERT: A 227 PHE cc_start: 0.7739 (t80) cc_final: 0.7442 (m-10) REVERT: A 228 ASN cc_start: 0.8446 (m-40) cc_final: 0.8078 (m110) REVERT: C 34 GLN cc_start: 0.6953 (tt0) cc_final: 0.6694 (pm20) REVERT: D 65 TRP cc_start: 0.7428 (m-10) cc_final: 0.6777 (t-100) REVERT: D 81 LYS cc_start: 0.4772 (OUTLIER) cc_final: 0.4276 (tppt) REVERT: D 110 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5699 (pp20) REVERT: D 228 ASN cc_start: 0.8515 (m-40) cc_final: 0.8157 (m110) REVERT: E 34 GLN cc_start: 0.6958 (tt0) cc_final: 0.6658 (pm20) REVERT: F 27 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: F 65 TRP cc_start: 0.7439 (m-10) cc_final: 0.6852 (t-100) REVERT: F 81 LYS cc_start: 0.4607 (OUTLIER) cc_final: 0.4099 (tppt) REVERT: F 101 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8511 (mt) REVERT: F 110 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5346 (pp20) REVERT: H 65 TRP cc_start: 0.7511 (m-10) cc_final: 0.6875 (t-100) REVERT: H 81 LYS cc_start: 0.4534 (OUTLIER) cc_final: 0.4071 (tppt) REVERT: H 110 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5291 (pp20) REVERT: H 228 ASN cc_start: 0.8253 (m-40) cc_final: 0.8037 (m110) outliers start: 49 outliers final: 31 residues processed: 278 average time/residue: 0.0815 time to fit residues: 32.9196 Evaluate side-chains 260 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 118 LEU 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 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 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 101 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 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 118 LEU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 167 MET Chi-restraints excluded: chain H residue 213 LEU 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: 0.5980 chunk 73 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4063 r_free = 0.4063 target = 0.163324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111605 restraints weight = 13229.960| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.09 r_work: 0.3220 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4862 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= 0.136 Angle : 0.705 13.079 12668 Z= 0.334 Chirality : 0.042 0.188 1424 Planarity : 0.003 0.028 1464 Dihedral : 17.639 116.995 1676 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.94 % Allowed : 33.30 % Favored : 61.76 % 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: 0.88 (0.27), residues: 1028 helix: 1.53 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.84 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 29 TYR 0.014 0.001 TYR D 57 PHE 0.032 0.001 PHE F 105 TRP 0.011 0.001 TRP A 196 HIS 0.002 0.001 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9392) covalent geometry : angle 0.70262 (12644) SS BOND : bond 0.00212 ( 12) SS BOND : angle 1.58222 ( 24) hydrogen bonds : bond 0.03513 ( 464) hydrogen bonds : angle 4.42594 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.95 seconds wall clock time: 44 minutes 13.47 seconds (2653.47 seconds total)