Starting phenix.real_space_refine on Sun Jul 27 12:48:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6o_21560/07_2025/6w6o_21560_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6o_21560/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w6o_21560/07_2025/6w6o_21560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6o_21560/07_2025/6w6o_21560.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6o_21560/07_2025/6w6o_21560_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6o_21560/07_2025/6w6o_21560_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.64, per 1000 atoms: 0.61 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: 2.52 Conformation dependent library (CDL) restraints added in 819.9 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: 0.80 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: 2.29 Time building geometry restraints manager: 2.81 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: 0.06 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 1.240 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.260 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP I 30 HIS 0.002 0.001 HIS D 52 PHE 0.012 0.001 PHE A 215 TYR 0.010 0.002 TYR D 57 ARG 0.002 0.000 ARG D 202 Details of bonding type rmsd hydrogen bonds : bond 0.15946 ( 464) hydrogen bonds : angle 8.12793 ( 1392) SS BOND : bond 0.00123 ( 12) SS BOND : angle 1.37695 ( 24) covalent geometry : bond 0.01078 ( 9392) covalent geometry : angle 1.33609 (12644) *********************** 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 : 0.956 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: 0.2229 time to fit residues: 113.4640 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 : 1.049 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 149 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 149 ASN H 179 ASN H 237 ASN I 10 ASN I 15 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107635 restraints weight = 13194.796| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.04 r_work: 0.3174 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9404 Z= 0.148 Angle : 0.664 6.647 12668 Z= 0.341 Chirality : 0.044 0.180 1424 Planarity : 0.004 0.028 1464 Dihedral : 22.611 146.415 1847 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 9.35 % Allowed : 22.06 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.26), residues: 1028 helix: -0.25 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.88 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 30 HIS 0.004 0.001 HIS A 52 PHE 0.015 0.001 PHE A 227 TYR 0.006 0.001 TYR H 57 ARG 0.002 0.000 ARG H 125 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 464) hydrogen bonds : angle 4.90114 ( 1392) SS BOND : bond 0.00290 ( 12) SS BOND : angle 2.11482 ( 24) covalent geometry : bond 0.00336 ( 9392) covalent geometry : angle 0.65807 (12644) *********************** 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 340 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 251 time to evaluate : 1.027 Fit side-chains REVERT: A 110 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.5735 (pp20) REVERT: A 149 ASN cc_start: 0.8789 (m-40) cc_final: 0.8579 (m-40) REVERT: A 227 PHE cc_start: 0.8085 (t80) cc_final: 0.7692 (m-10) REVERT: C 7 LYS cc_start: 0.6657 (mmtp) cc_final: 0.6239 (mmtm) REVERT: D 110 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.5796 (pp20) REVERT: E 7 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6869 (mmtm) REVERT: F 110 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.5721 (pp20) REVERT: F 149 ASN cc_start: 0.8792 (m110) cc_final: 0.8565 (m-40) REVERT: G 7 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6850 (mmtm) REVERT: G 23 VAL cc_start: 0.7114 (OUTLIER) cc_final: 0.6905 (p) REVERT: H 110 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5773 (pp20) REVERT: I 7 LYS cc_start: 0.6742 (mmtp) cc_final: 0.6319 (mmtm) REVERT: I 22 LEU cc_start: 0.6809 (mt) cc_final: 0.6590 (mt) outliers start: 89 outliers final: 48 residues processed: 329 average time/residue: 0.2092 time to fit residues: 95.0264 Evaluate side-chains 284 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 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 61 LEU 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 E residue 33 TYR Chi-restraints excluded: chain F residue 61 LEU 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 G residue 23 VAL Chi-restraints excluded: chain H residue 61 LEU 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 18 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS 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 H 237 ASN I 10 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.160578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108688 restraints weight = 13320.222| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.12 r_work: 0.3183 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9404 Z= 0.132 Angle : 0.629 9.047 12668 Z= 0.318 Chirality : 0.042 0.189 1424 Planarity : 0.003 0.022 1464 Dihedral : 20.490 91.006 1724 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 8.72 % Allowed : 22.06 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.27), residues: 1028 helix: 0.79 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -2.47 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 30 HIS 0.001 0.000 HIS D 22 PHE 0.011 0.001 PHE H 230 TYR 0.007 0.001 TYR H 57 ARG 0.004 0.000 ARG H 125 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 464) hydrogen bonds : angle 4.54456 ( 1392) SS BOND : bond 0.00672 ( 12) SS BOND : angle 2.55722 ( 24) covalent geometry : bond 0.00292 ( 9392) covalent geometry : angle 0.61991 (12644) *********************** 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 343 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 0.961 Fit side-chains REVERT: A 20 VAL cc_start: 0.6664 (OUTLIER) cc_final: 0.6442 (t) REVERT: A 110 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5804 (pp20) REVERT: A 227 PHE cc_start: 0.7962 (t80) cc_final: 0.7505 (m-10) REVERT: C 17 CYS cc_start: 0.5811 (t) cc_final: 0.5445 (m) REVERT: D 20 VAL cc_start: 0.6721 (OUTLIER) cc_final: 0.6511 (t) REVERT: D 100 SER cc_start: 0.8002 (m) cc_final: 0.7781 (m) REVERT: D 110 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5986 (pp20) REVERT: E 7 LYS cc_start: 0.7034 (mmtt) cc_final: 0.6828 (mmtm) REVERT: E 17 CYS cc_start: 0.5781 (t) cc_final: 0.5565 (m) REVERT: E 27 LYS cc_start: 0.7482 (tppt) cc_final: 0.7270 (tppt) REVERT: F 20 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6352 (t) REVERT: F 100 SER cc_start: 0.8073 (m) cc_final: 0.7869 (m) REVERT: F 110 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.5867 (pp20) REVERT: H 20 VAL cc_start: 0.6796 (OUTLIER) cc_final: 0.6581 (t) REVERT: H 110 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5869 (pp20) outliers start: 83 outliers final: 43 residues processed: 331 average time/residue: 0.1874 time to fit residues: 87.5126 Evaluate side-chains 292 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 TRP 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 229 LEU Chi-restraints excluded: chain C residue 13 ASN 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 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 F residue 20 VAL Chi-restraints excluded: chain F residue 65 TRP 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 167 MET Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 236 ASN 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 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 194 GLU 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 59 optimal weight: 0.0570 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 C 10 ASN C 15 GLN C 34 GLN D 22 HIS D 36 ASN D 149 ASN D 228 ASN D 237 ASN E 10 ASN E 15 GLN E 34 GLN F 36 ASN F 228 ASN G 10 ASN H 36 ASN H 228 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109695 restraints weight = 13228.401| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.09 r_work: 0.3198 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9404 Z= 0.125 Angle : 0.629 8.830 12668 Z= 0.307 Chirality : 0.041 0.175 1424 Planarity : 0.003 0.022 1464 Dihedral : 19.910 87.629 1700 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 9.77 % Allowed : 25.32 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 1028 helix: 0.96 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.13 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 30 HIS 0.001 0.000 HIS F 22 PHE 0.010 0.001 PHE A 227 TYR 0.005 0.001 TYR I 33 ARG 0.003 0.000 ARG H 125 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 464) hydrogen bonds : angle 4.49900 ( 1392) SS BOND : bond 0.00413 ( 12) SS BOND : angle 1.68635 ( 24) covalent geometry : bond 0.00274 ( 9392) covalent geometry : angle 0.62544 (12644) *********************** 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 344 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 251 time to evaluate : 0.943 Fit side-chains REVERT: A 27 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: A 110 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5899 (pp20) REVERT: A 227 PHE cc_start: 0.7969 (t80) cc_final: 0.7578 (m-80) REVERT: C 34 GLN cc_start: 0.6936 (tt0) cc_final: 0.6726 (tt0) REVERT: D 27 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: D 110 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5988 (pp20) REVERT: D 228 ASN cc_start: 0.8486 (m-40) cc_final: 0.8280 (m110) REVERT: F 27 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: F 110 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5668 (pp20) REVERT: F 228 ASN cc_start: 0.8542 (m-40) cc_final: 0.8342 (m110) REVERT: H 20 VAL cc_start: 0.6694 (OUTLIER) cc_final: 0.6480 (t) REVERT: H 27 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: H 90 ASN cc_start: 0.8786 (m-40) cc_final: 0.8442 (m110) REVERT: H 110 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5690 (pp20) REVERT: H 228 ASN cc_start: 0.8489 (m-40) cc_final: 0.8259 (m110) outliers start: 93 outliers final: 51 residues processed: 318 average time/residue: 0.1909 time to fit residues: 85.7453 Evaluate side-chains 302 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 213 LEU 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 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 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 99 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 213 LEU 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 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 213 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.160886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108619 restraints weight = 13150.621| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.08 r_work: 0.3175 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4048 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= 0.141 Angle : 0.649 9.368 12668 Z= 0.317 Chirality : 0.042 0.152 1424 Planarity : 0.003 0.022 1464 Dihedral : 19.688 93.369 1700 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 7.88 % Allowed : 28.36 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 1028 helix: 1.17 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 30 HIS 0.001 0.000 HIS F 171 PHE 0.022 0.001 PHE H 105 TYR 0.010 0.001 TYR H 57 ARG 0.002 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 464) hydrogen bonds : angle 4.50284 ( 1392) SS BOND : bond 0.00442 ( 12) SS BOND : angle 2.48783 ( 24) covalent geometry : bond 0.00324 ( 9392) covalent geometry : angle 0.64014 (12644) *********************** 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 318 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 0.873 Fit side-chains REVERT: A 27 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: A 110 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.5993 (pp20) REVERT: A 227 PHE cc_start: 0.7937 (t80) cc_final: 0.7543 (m-80) REVERT: D 110 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6003 (pp20) REVERT: E 34 GLN cc_start: 0.6860 (tt0) cc_final: 0.6453 (pm20) REVERT: F 27 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: F 110 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5648 (pp20) REVERT: F 228 ASN cc_start: 0.8568 (m-40) cc_final: 0.8358 (m110) REVERT: H 27 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: H 90 ASN cc_start: 0.8790 (m-40) cc_final: 0.8462 (m110) REVERT: H 110 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5683 (pp20) REVERT: H 228 ASN cc_start: 0.8439 (m-40) cc_final: 0.8206 (m110) outliers start: 75 outliers final: 43 residues processed: 298 average time/residue: 0.1996 time to fit residues: 83.7145 Evaluate side-chains 281 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 167 MET Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 13 ASN 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 213 LEU 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 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 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 88 SER 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 13 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 D 228 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.162140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110536 restraints weight = 13097.504| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.07 r_work: 0.3198 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9404 Z= 0.125 Angle : 0.636 9.244 12668 Z= 0.307 Chirality : 0.041 0.136 1424 Planarity : 0.003 0.022 1464 Dihedral : 19.035 95.781 1700 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 6.20 % Allowed : 31.72 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1028 helix: 1.36 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.95 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.001 0.000 HIS F 22 PHE 0.019 0.001 PHE H 105 TYR 0.016 0.001 TYR D 57 ARG 0.002 0.000 ARG F 202 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 464) hydrogen bonds : angle 4.44628 ( 1392) SS BOND : bond 0.00248 ( 12) SS BOND : angle 1.97557 ( 24) covalent geometry : bond 0.00278 ( 9392) covalent geometry : angle 0.63088 (12644) *********************** 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 302 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 1.098 Fit side-chains REVERT: A 27 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: A 65 TRP cc_start: 0.7636 (OUTLIER) cc_final: 0.6962 (t-100) REVERT: A 110 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5964 (pp20) REVERT: A 227 PHE cc_start: 0.7878 (t80) cc_final: 0.7420 (m-80) REVERT: C 34 GLN cc_start: 0.6950 (tt0) cc_final: 0.6557 (pm20) REVERT: D 65 TRP cc_start: 0.7585 (m-10) cc_final: 0.6873 (t-100) REVERT: D 110 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6011 (pp20) REVERT: E 34 GLN cc_start: 0.6919 (tt0) cc_final: 0.6526 (pm20) REVERT: F 27 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: F 65 TRP cc_start: 0.7602 (m-10) cc_final: 0.6890 (t-100) REVERT: F 110 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5569 (pp20) REVERT: F 228 ASN cc_start: 0.8530 (m-40) cc_final: 0.8264 (m110) REVERT: H 27 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: H 65 TRP cc_start: 0.7690 (m-10) cc_final: 0.6919 (t-100) REVERT: H 90 ASN cc_start: 0.8763 (m-40) cc_final: 0.8429 (m110) REVERT: H 110 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5543 (pp20) REVERT: H 228 ASN cc_start: 0.8294 (m-40) cc_final: 0.8061 (m110) outliers start: 59 outliers final: 37 residues processed: 282 average time/residue: 0.2126 time to fit residues: 83.2523 Evaluate side-chains 272 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 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 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 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 38 optimal weight: 4.9990 chunk 6 optimal weight: 0.0170 chunk 11 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 F 17 GLN G 10 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.163359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111660 restraints weight = 13285.500| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.11 r_work: 0.3220 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9404 Z= 0.119 Angle : 0.650 9.530 12668 Z= 0.310 Chirality : 0.040 0.130 1424 Planarity : 0.003 0.021 1464 Dihedral : 18.525 98.383 1692 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.88 % Allowed : 33.19 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1028 helix: 1.48 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.83 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 30 HIS 0.002 0.000 HIS F 22 PHE 0.017 0.001 PHE A 105 TYR 0.018 0.001 TYR H 57 ARG 0.003 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 464) hydrogen bonds : angle 4.42914 ( 1392) SS BOND : bond 0.00195 ( 12) SS BOND : angle 1.78746 ( 24) covalent geometry : bond 0.00258 ( 9392) covalent geometry : angle 0.64621 (12644) *********************** 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 291 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 0.970 Fit side-chains REVERT: A 27 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: A 65 TRP cc_start: 0.7602 (OUTLIER) cc_final: 0.6947 (t-100) REVERT: A 81 LYS cc_start: 0.4592 (OUTLIER) cc_final: 0.4104 (tppt) REVERT: A 90 ASN cc_start: 0.8744 (m-40) cc_final: 0.8420 (m-40) REVERT: A 110 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5811 (pp20) REVERT: A 202 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8649 (mmt180) REVERT: A 227 PHE cc_start: 0.7804 (t80) cc_final: 0.7435 (m-10) REVERT: C 34 GLN cc_start: 0.6904 (tt0) cc_final: 0.6609 (pm20) REVERT: D 49 TYR cc_start: 0.8091 (t80) cc_final: 0.6893 (t80) REVERT: D 65 TRP cc_start: 0.7660 (OUTLIER) cc_final: 0.6966 (t-100) REVERT: D 81 LYS cc_start: 0.4766 (OUTLIER) cc_final: 0.4292 (tppt) REVERT: D 110 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5866 (pp20) REVERT: E 34 GLN cc_start: 0.6905 (tt0) cc_final: 0.6518 (pm20) REVERT: F 27 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: F 49 TYR cc_start: 0.8079 (t80) cc_final: 0.6870 (t80) REVERT: F 65 TRP cc_start: 0.7611 (OUTLIER) cc_final: 0.6902 (t-100) REVERT: F 81 LYS cc_start: 0.4628 (OUTLIER) cc_final: 0.4115 (tppt) REVERT: F 110 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5470 (pp20) REVERT: F 228 ASN cc_start: 0.8491 (m-40) cc_final: 0.8218 (m110) REVERT: H 27 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: H 65 TRP cc_start: 0.7688 (OUTLIER) cc_final: 0.6971 (t-100) REVERT: H 81 LYS cc_start: 0.4623 (OUTLIER) cc_final: 0.4102 (tppt) REVERT: H 90 ASN cc_start: 0.8751 (m-40) cc_final: 0.8418 (m-40) REVERT: H 110 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5444 (pp20) REVERT: H 202 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8543 (mmt180) REVERT: H 228 ASN cc_start: 0.8276 (m-40) cc_final: 0.8038 (m110) outliers start: 56 outliers final: 30 residues processed: 273 average time/residue: 0.2000 time to fit residues: 76.1325 Evaluate side-chains 264 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 213 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 140 LEU 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 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 229 LEU 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 55 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 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 36 ASN C 10 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.161486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109077 restraints weight = 13390.204| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.10 r_work: 0.3184 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9404 Z= 0.140 Angle : 0.666 8.786 12668 Z= 0.318 Chirality : 0.041 0.121 1424 Planarity : 0.003 0.021 1464 Dihedral : 18.721 101.419 1686 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.20 % Allowed : 32.14 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1028 helix: 1.47 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 196 HIS 0.002 0.001 HIS F 22 PHE 0.025 0.001 PHE A 105 TYR 0.019 0.001 TYR D 57 ARG 0.003 0.000 ARG F 202 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 464) hydrogen bonds : angle 4.47722 ( 1392) SS BOND : bond 0.00291 ( 12) SS BOND : angle 1.80098 ( 24) covalent geometry : bond 0.00323 ( 9392) covalent geometry : angle 0.66198 (12644) *********************** 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 288 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 1.099 Fit side-chains REVERT: A 27 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: A 81 LYS cc_start: 0.4663 (OUTLIER) cc_final: 0.4124 (tppt) REVERT: A 90 ASN cc_start: 0.8717 (m-40) cc_final: 0.8399 (m110) REVERT: A 110 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.5955 (pp20) REVERT: A 227 PHE cc_start: 0.7874 (t80) cc_final: 0.7475 (m-10) REVERT: C 34 GLN cc_start: 0.6864 (tt0) cc_final: 0.6489 (pm20) REVERT: D 65 TRP cc_start: 0.7544 (m-10) cc_final: 0.6915 (t-100) REVERT: D 81 LYS cc_start: 0.4815 (OUTLIER) cc_final: 0.4290 (tppt) REVERT: D 90 ASN cc_start: 0.8713 (m-40) cc_final: 0.8386 (m110) REVERT: D 110 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5966 (pp20) REVERT: E 34 GLN cc_start: 0.6786 (tt0) cc_final: 0.6361 (pm20) REVERT: F 27 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: F 65 TRP cc_start: 0.7541 (m-10) cc_final: 0.6856 (t-100) REVERT: F 81 LYS cc_start: 0.4681 (OUTLIER) cc_final: 0.4119 (tppt) REVERT: F 110 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5459 (pp20) REVERT: F 228 ASN cc_start: 0.8548 (m-40) cc_final: 0.8279 (m110) REVERT: H 27 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: H 81 LYS cc_start: 0.4676 (OUTLIER) cc_final: 0.4108 (tppt) REVERT: H 90 ASN cc_start: 0.8749 (m-40) cc_final: 0.8443 (m-40) REVERT: H 110 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5480 (pp20) REVERT: H 228 ASN cc_start: 0.8259 (m-40) cc_final: 0.8049 (m110) outliers start: 59 outliers final: 34 residues processed: 267 average time/residue: 0.1984 time to fit residues: 74.3745 Evaluate side-chains 262 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 167 MET Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 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 167 MET 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 73 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 H 237 ASN I 10 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.159798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107133 restraints weight = 13115.364| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.07 r_work: 0.3147 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9404 Z= 0.164 Angle : 0.689 8.461 12668 Z= 0.333 Chirality : 0.042 0.129 1424 Planarity : 0.004 0.024 1464 Dihedral : 18.972 106.081 1686 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.78 % Allowed : 32.25 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 1028 helix: 1.47 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 196 HIS 0.002 0.001 HIS F 22 PHE 0.024 0.002 PHE F 105 TYR 0.022 0.002 TYR A 57 ARG 0.003 0.000 ARG I 29 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 464) hydrogen bonds : angle 4.58914 ( 1392) SS BOND : bond 0.00194 ( 12) SS BOND : angle 1.73111 ( 24) covalent geometry : bond 0.00387 ( 9392) covalent geometry : angle 0.68502 (12644) *********************** 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 284 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 0.953 Fit side-chains REVERT: A 27 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: A 90 ASN cc_start: 0.8749 (m-40) cc_final: 0.8447 (m110) REVERT: A 110 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6036 (pp20) REVERT: A 227 PHE cc_start: 0.7918 (t80) cc_final: 0.7500 (m-10) REVERT: C 34 GLN cc_start: 0.6831 (tt0) cc_final: 0.6416 (pm20) REVERT: D 65 TRP cc_start: 0.7552 (m-10) cc_final: 0.6953 (t-100) REVERT: D 90 ASN cc_start: 0.8729 (m-40) cc_final: 0.8421 (m110) REVERT: D 110 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6043 (pp20) REVERT: E 34 GLN cc_start: 0.6898 (tt0) cc_final: 0.6504 (pm20) REVERT: F 27 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: F 65 TRP cc_start: 0.7579 (m-10) cc_final: 0.6990 (t-100) REVERT: F 90 ASN cc_start: 0.8751 (m-40) cc_final: 0.8433 (m110) REVERT: F 110 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5646 (pp20) REVERT: F 228 ASN cc_start: 0.8534 (m-40) cc_final: 0.8260 (m110) REVERT: H 27 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: H 90 ASN cc_start: 0.8762 (m-40) cc_final: 0.8453 (m110) REVERT: H 110 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5619 (pp20) REVERT: H 228 ASN cc_start: 0.8320 (m-40) cc_final: 0.8102 (m110) outliers start: 55 outliers final: 35 residues processed: 265 average time/residue: 0.1892 time to fit residues: 70.8170 Evaluate side-chains 266 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 202 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 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 167 MET 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 88 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 0.0060 chunk 95 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.162300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109930 restraints weight = 13334.572| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.11 r_work: 0.3188 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9404 Z= 0.123 Angle : 0.661 8.588 12668 Z= 0.317 Chirality : 0.040 0.142 1424 Planarity : 0.003 0.024 1464 Dihedral : 18.160 112.143 1686 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.04 % Allowed : 32.14 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 1028 helix: 1.54 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 196 HIS 0.002 0.001 HIS F 22 PHE 0.023 0.001 PHE H 105 TYR 0.016 0.001 TYR A 57 ARG 0.003 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 464) hydrogen bonds : angle 4.49023 ( 1392) SS BOND : bond 0.00147 ( 12) SS BOND : angle 1.68110 ( 24) covalent geometry : bond 0.00269 ( 9392) covalent geometry : angle 0.65798 (12644) ********************** 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 277 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 1.047 Fit side-chains REVERT: A 27 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: A 65 TRP cc_start: 0.7501 (m-10) cc_final: 0.6870 (t-100) REVERT: A 81 LYS cc_start: 0.4659 (OUTLIER) cc_final: 0.4097 (tppt) REVERT: A 110 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5929 (pp20) REVERT: A 227 PHE cc_start: 0.7865 (t80) cc_final: 0.7481 (m-10) REVERT: C 34 GLN cc_start: 0.6857 (tt0) cc_final: 0.6404 (pm20) REVERT: D 49 TYR cc_start: 0.8106 (t80) cc_final: 0.6901 (t80) REVERT: D 65 TRP cc_start: 0.7467 (m-10) cc_final: 0.6901 (t-100) REVERT: D 81 LYS cc_start: 0.4656 (OUTLIER) cc_final: 0.4111 (tppt) REVERT: D 110 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5918 (pp20) REVERT: D 202 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8636 (mmt180) REVERT: E 34 GLN cc_start: 0.6982 (tt0) cc_final: 0.6562 (pm20) REVERT: F 27 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: F 49 TYR cc_start: 0.8079 (t80) cc_final: 0.6879 (t80) REVERT: F 65 TRP cc_start: 0.7342 (m-10) cc_final: 0.6802 (t-100) REVERT: F 81 LYS cc_start: 0.4686 (OUTLIER) cc_final: 0.4102 (tppt) REVERT: F 110 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5482 (pp20) REVERT: F 228 ASN cc_start: 0.8433 (m-40) cc_final: 0.8071 (m110) REVERT: H 27 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: H 65 TRP cc_start: 0.7519 (m-10) cc_final: 0.6928 (t-100) REVERT: H 81 LYS cc_start: 0.4635 (OUTLIER) cc_final: 0.4082 (tppt) REVERT: H 90 ASN cc_start: 0.8714 (m-40) cc_final: 0.8398 (m110) REVERT: H 110 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5439 (pp20) REVERT: H 228 ASN cc_start: 0.8194 (m-40) cc_final: 0.7972 (m110) outliers start: 48 outliers final: 29 residues processed: 263 average time/residue: 0.1972 time to fit residues: 75.3750 Evaluate side-chains 261 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 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 167 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 36 ASN ** H 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.161652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109052 restraints weight = 13152.125| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.08 r_work: 0.3178 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4782 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= 0.134 Angle : 0.681 12.515 12668 Z= 0.326 Chirality : 0.042 0.186 1424 Planarity : 0.003 0.026 1464 Dihedral : 18.086 114.504 1682 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.46 % Allowed : 32.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 1028 helix: 1.77 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 196 HIS 0.002 0.001 HIS H 22 PHE 0.023 0.001 PHE F 105 TYR 0.014 0.001 TYR A 57 ARG 0.003 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 464) hydrogen bonds : angle 4.58092 ( 1392) SS BOND : bond 0.00157 ( 12) SS BOND : angle 1.57618 ( 24) covalent geometry : bond 0.00305 ( 9392) covalent geometry : angle 0.67775 (12644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5589.26 seconds wall clock time: 96 minutes 27.53 seconds (5787.53 seconds total)