Starting phenix.real_space_refine on Fri Mar 14 00:05:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6o_21560/03_2025/6w6o_21560_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6o_21560/03_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_21560/03_2025/6w6o_21560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6o_21560/03_2025/6w6o_21560.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6o_21560/03_2025/6w6o_21560_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6o_21560/03_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-5624/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: 5.19, per 1000 atoms: 0.57 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: 2.41 Conformation dependent library (CDL) restraints added in 970.7 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: 0.70 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: 2.08 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: 0.010 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.650 Find NCS groups from input model: 0.160 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- 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 9392 Z= 0.682 Angle : 1.336 11.566 12644 Z= 0.605 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 *********************** 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 : 1.024 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: 0.2642 time to fit residues: 134.4609 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 : 1.258 ------------------------------------------------------------------------------- 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: 4.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 179 ASN H 237 ASN I 10 ASN I 15 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106160 restraints weight = 13186.339| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.07 r_work: 0.3148 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9392 Z= 0.247 Angle : 0.677 7.012 12644 Z= 0.348 Chirality : 0.045 0.181 1424 Planarity : 0.004 0.029 1464 Dihedral : 22.878 146.276 1847 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 9.35 % Allowed : 22.27 % Favored : 68.38 % 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: -1.84 (0.26), residues: 1028 helix: -0.33 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.91 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 30 HIS 0.003 0.001 HIS H 52 PHE 0.015 0.001 PHE A 227 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG A 125 *********************** 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 336 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 247 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.5754 (pp20) REVERT: A 227 PHE cc_start: 0.8083 (t80) cc_final: 0.7683 (m-10) REVERT: C 7 LYS cc_start: 0.6736 (mmtp) cc_final: 0.6311 (mmtm) REVERT: D 110 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.5799 (pp20) REVERT: E 7 LYS cc_start: 0.7080 (mmtt) cc_final: 0.6858 (mmtm) REVERT: F 110 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.5712 (pp20) REVERT: G 7 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6824 (mmtm) REVERT: H 110 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5801 (pp20) REVERT: I 7 LYS cc_start: 0.6710 (mmtp) cc_final: 0.6293 (mmtm) REVERT: I 22 LEU cc_start: 0.6779 (mt) cc_final: 0.6579 (mt) outliers start: 89 outliers final: 45 residues processed: 325 average time/residue: 0.2441 time to fit residues: 110.5988 Evaluate side-chains 280 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 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 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 234 ILE Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.159971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108476 restraints weight = 13367.847| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.08 r_work: 0.3184 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9392 Z= 0.192 Angle : 0.623 9.052 12644 Z= 0.316 Chirality : 0.042 0.195 1424 Planarity : 0.003 0.023 1464 Dihedral : 20.658 93.807 1718 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 8.82 % Allowed : 22.90 % Favored : 68.28 % 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: 0.78 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -2.45 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 30 HIS 0.001 0.000 HIS H 22 PHE 0.013 0.001 PHE H 230 TYR 0.008 0.001 TYR F 57 ARG 0.003 0.000 ARG D 125 *********************** 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 339 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 255 time to evaluate : 1.087 Fit side-chains REVERT: A 20 VAL cc_start: 0.6622 (OUTLIER) cc_final: 0.6393 (t) REVERT: A 27 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: A 110 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5800 (pp20) REVERT: A 227 PHE cc_start: 0.7948 (t80) cc_final: 0.7546 (m-10) REVERT: A 228 ASN cc_start: 0.8691 (m-40) cc_final: 0.8455 (m110) REVERT: C 7 LYS cc_start: 0.6839 (mmtp) cc_final: 0.6576 (mmtm) REVERT: C 17 CYS cc_start: 0.5746 (t) cc_final: 0.5362 (m) REVERT: D 20 VAL cc_start: 0.6730 (OUTLIER) cc_final: 0.6522 (t) REVERT: D 27 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: D 100 SER cc_start: 0.8009 (m) cc_final: 0.7782 (m) REVERT: D 110 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6002 (pp20) REVERT: E 7 LYS cc_start: 0.7030 (mmtt) cc_final: 0.6821 (mmtm) REVERT: E 17 CYS cc_start: 0.5688 (t) cc_final: 0.5466 (m) REVERT: F 27 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: F 100 SER cc_start: 0.8096 (m) cc_final: 0.7883 (m) REVERT: F 110 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5912 (pp20) REVERT: H 20 VAL cc_start: 0.6809 (OUTLIER) cc_final: 0.6588 (t) REVERT: H 27 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: H 100 SER cc_start: 0.7991 (m) cc_final: 0.7789 (m) REVERT: H 110 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5905 (pp20) outliers start: 84 outliers final: 35 residues processed: 325 average time/residue: 0.2129 time to fit residues: 98.9240 Evaluate side-chains 288 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 21 optimal weight: 0.6980 chunk 98 optimal weight: 0.0870 chunk 92 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 149 ASN A 237 ASN C 10 ASN C 34 GLN D 22 HIS D 36 ASN D 149 ASN D 228 ASN D 237 ASN E 10 ASN F 36 ASN F 228 ASN G 10 ASN G 34 GLN H 36 ASN H 149 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 = 0.4055 r_free = 0.4055 target = 0.162370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110794 restraints weight = 13283.080| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.13 r_work: 0.3213 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9392 Z= 0.157 Angle : 0.617 8.635 12644 Z= 0.300 Chirality : 0.041 0.174 1424 Planarity : 0.003 0.021 1464 Dihedral : 19.796 87.373 1702 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 8.72 % Allowed : 25.53 % Favored : 65.76 % 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: 0.06 (0.27), residues: 1028 helix: 1.04 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.15 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 30 HIS 0.001 0.000 HIS F 22 PHE 0.009 0.001 PHE H 230 TYR 0.004 0.001 TYR A 57 ARG 0.003 0.000 ARG F 125 *********************** 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 335 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 252 time to evaluate : 1.011 Fit side-chains REVERT: A 110 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5932 (pp20) REVERT: A 227 PHE cc_start: 0.7887 (t80) cc_final: 0.7512 (m-80) REVERT: C 34 GLN cc_start: 0.6935 (tt0) cc_final: 0.6719 (tt0) REVERT: D 20 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.6743 (t) REVERT: D 90 ASN cc_start: 0.8758 (m-40) cc_final: 0.8406 (m110) REVERT: D 110 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5955 (pp20) REVERT: E 34 GLN cc_start: 0.6853 (tt0) cc_final: 0.6355 (pm20) REVERT: F 100 SER cc_start: 0.7968 (m) cc_final: 0.7522 (p) REVERT: F 110 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5652 (pp20) REVERT: F 228 ASN cc_start: 0.8538 (m-40) cc_final: 0.8308 (m110) REVERT: G 34 GLN cc_start: 0.6785 (tt0) cc_final: 0.6093 (pt0) REVERT: H 20 VAL cc_start: 0.6724 (OUTLIER) cc_final: 0.6510 (t) REVERT: H 100 SER cc_start: 0.7991 (m) cc_final: 0.7566 (p) REVERT: H 110 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5593 (pp20) REVERT: H 228 ASN cc_start: 0.8434 (m-40) cc_final: 0.8088 (m110) outliers start: 83 outliers final: 41 residues processed: 318 average time/residue: 0.1873 time to fit residues: 84.3587 Evaluate side-chains 286 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 61 LEU 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 G residue 16 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN D 228 ASN D 237 ASN E 10 ASN G 10 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107023 restraints weight = 13076.886| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.12 r_work: 0.3155 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9392 Z= 0.234 Angle : 0.640 8.875 12644 Z= 0.314 Chirality : 0.042 0.155 1424 Planarity : 0.003 0.021 1464 Dihedral : 19.809 93.294 1698 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.98 % Allowed : 27.94 % Favored : 64.08 % 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: -0.01 (0.27), residues: 1028 helix: 1.15 (0.20), residues: 700 sheet: -3.94 (0.62), residues: 48 loop : -2.24 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 30 HIS 0.001 0.000 HIS D 171 PHE 0.023 0.001 PHE D 105 TYR 0.016 0.001 TYR F 57 ARG 0.003 0.000 ARG F 125 *********************** 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 321 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 245 time to evaluate : 1.006 Fit side-chains REVERT: A 27 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: A 90 ASN cc_start: 0.8751 (m-40) cc_final: 0.8421 (m110) REVERT: A 110 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5993 (pp20) REVERT: A 227 PHE cc_start: 0.7874 (t80) cc_final: 0.7492 (m-80) REVERT: D 20 VAL cc_start: 0.6578 (OUTLIER) cc_final: 0.6367 (t) REVERT: D 90 ASN cc_start: 0.8810 (m-40) cc_final: 0.8488 (m110) REVERT: D 110 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6012 (pp20) REVERT: E 34 GLN cc_start: 0.6922 (tt0) cc_final: 0.6482 (pm20) REVERT: F 27 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: F 90 ASN cc_start: 0.8801 (m-40) cc_final: 0.8480 (m110) REVERT: F 100 SER cc_start: 0.8128 (m) cc_final: 0.7890 (m) REVERT: F 110 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5761 (pp20) REVERT: F 228 ASN cc_start: 0.8605 (m-40) cc_final: 0.8391 (m110) REVERT: G 34 GLN cc_start: 0.6713 (tt0) cc_final: 0.6056 (pt0) REVERT: H 27 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: H 90 ASN cc_start: 0.8798 (m-40) cc_final: 0.8469 (m110) REVERT: H 100 SER cc_start: 0.8150 (m) cc_final: 0.7915 (m) REVERT: H 110 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5658 (pp20) REVERT: H 228 ASN cc_start: 0.8436 (m-40) cc_final: 0.8221 (m110) outliers start: 76 outliers final: 43 residues processed: 303 average time/residue: 0.1880 time to fit residues: 79.8711 Evaluate side-chains 283 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 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 213 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 22 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN C 34 GLN D 36 ASN E 10 ASN F 36 ASN G 10 ASN H 36 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.156428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103477 restraints weight = 13128.200| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.09 r_work: 0.3089 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9392 Z= 0.397 Angle : 0.711 8.613 12644 Z= 0.353 Chirality : 0.045 0.138 1424 Planarity : 0.004 0.024 1464 Dihedral : 21.087 110.321 1698 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 6.72 % Allowed : 30.15 % Favored : 63.13 % 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: 0.24 (0.27), residues: 1028 helix: 1.08 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.81 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 196 HIS 0.002 0.001 HIS F 171 PHE 0.019 0.002 PHE H 105 TYR 0.026 0.002 TYR A 57 ARG 0.003 0.000 ARG F 202 *********************** 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 289 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 1.041 Fit side-chains REVERT: A 27 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: A 90 ASN cc_start: 0.8802 (m-40) cc_final: 0.8525 (m110) REVERT: A 110 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6139 (pp20) REVERT: A 227 PHE cc_start: 0.8081 (t80) cc_final: 0.7602 (m-80) REVERT: D 27 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: D 90 ASN cc_start: 0.8816 (m-40) cc_final: 0.8515 (m110) REVERT: D 110 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6167 (pp20) REVERT: F 27 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: F 90 ASN cc_start: 0.8794 (m-40) cc_final: 0.8513 (m110) REVERT: F 110 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.5836 (pp20) REVERT: H 27 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: H 90 ASN cc_start: 0.8795 (m-40) cc_final: 0.8518 (m110) REVERT: H 110 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5683 (pp20) outliers start: 64 outliers final: 40 residues processed: 276 average time/residue: 0.1955 time to fit residues: 75.8230 Evaluate side-chains 261 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 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 184 LEU 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 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 184 LEU 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 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 184 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 228 ASN G 10 ASN G 34 GLN H 228 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.160200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108149 restraints weight = 13279.149| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.11 r_work: 0.3167 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.199 Angle : 0.637 8.429 12644 Z= 0.314 Chirality : 0.041 0.141 1424 Planarity : 0.003 0.021 1464 Dihedral : 19.823 109.228 1694 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.99 % Allowed : 31.20 % 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: 0.57 (0.27), residues: 1028 helix: 1.31 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.75 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.001 0.001 HIS D 22 PHE 0.017 0.001 PHE H 105 TYR 0.017 0.001 TYR A 57 ARG 0.002 0.000 ARG A 202 *********************** 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 282 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 0.983 Fit side-chains REVERT: A 27 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: A 110 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5982 (pp20) REVERT: A 227 PHE cc_start: 0.7895 (t80) cc_final: 0.7426 (m-80) REVERT: C 34 GLN cc_start: 0.6802 (tt0) cc_final: 0.6557 (pm20) REVERT: D 110 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6127 (pp20) REVERT: E 34 GLN cc_start: 0.6730 (tt0) cc_final: 0.6516 (pm20) REVERT: F 27 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: F 65 TRP cc_start: 0.7693 (OUTLIER) cc_final: 0.6975 (t-100) REVERT: F 110 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5659 (pp20) REVERT: H 27 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: H 90 ASN cc_start: 0.8755 (m-40) cc_final: 0.8436 (m110) REVERT: H 110 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5538 (pp20) outliers start: 57 outliers final: 40 residues processed: 269 average time/residue: 0.2054 time to fit residues: 76.7887 Evaluate side-chains 261 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 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 202 ARG Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 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 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 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: 0.8980 chunk 73 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 G 34 GLN H 36 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109845 restraints weight = 13423.244| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.09 r_work: 0.3189 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.185 Angle : 0.642 9.863 12644 Z= 0.311 Chirality : 0.040 0.134 1424 Planarity : 0.003 0.021 1464 Dihedral : 18.903 116.444 1692 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 6.41 % Allowed : 30.67 % Favored : 62.92 % 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: 0.75 (0.27), residues: 1028 helix: 1.42 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.001 0.000 HIS A 22 PHE 0.015 0.001 PHE H 105 TYR 0.019 0.001 TYR F 57 ARG 0.002 0.000 ARG E 29 *********************** 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 287 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 226 time to evaluate : 1.117 Fit side-chains REVERT: A 27 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: A 65 TRP cc_start: 0.7561 (OUTLIER) cc_final: 0.6957 (t-100) REVERT: A 110 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6036 (pp20) REVERT: A 202 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8613 (mmt180) REVERT: A 227 PHE cc_start: 0.7797 (t80) cc_final: 0.7404 (m-10) REVERT: A 228 ASN cc_start: 0.8654 (m-40) cc_final: 0.8147 (m110) REVERT: C 34 GLN cc_start: 0.6725 (tt0) cc_final: 0.6447 (pm20) REVERT: D 65 TRP cc_start: 0.7551 (OUTLIER) cc_final: 0.6935 (t-100) REVERT: D 110 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5985 (pp20) REVERT: F 27 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: F 100 SER cc_start: 0.8156 (m) cc_final: 0.7926 (m) REVERT: F 110 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5638 (pp20) REVERT: H 27 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: H 90 ASN cc_start: 0.8730 (m-40) cc_final: 0.8431 (m110) REVERT: H 100 SER cc_start: 0.8136 (m) cc_final: 0.7887 (m) REVERT: H 110 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5402 (pp20) outliers start: 61 outliers final: 38 residues processed: 268 average time/residue: 0.2086 time to fit residues: 78.2772 Evaluate side-chains 259 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 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 184 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 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: 0.9980 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 I 10 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.161563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109619 restraints weight = 13153.633| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.09 r_work: 0.3187 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9392 Z= 0.201 Angle : 0.662 10.319 12644 Z= 0.320 Chirality : 0.041 0.132 1424 Planarity : 0.003 0.022 1464 Dihedral : 18.491 116.824 1680 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.15 % Allowed : 30.67 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.27), residues: 1028 helix: 1.47 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.63 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 30 HIS 0.001 0.001 HIS F 22 PHE 0.015 0.001 PHE H 105 TYR 0.018 0.001 TYR H 57 ARG 0.003 0.000 ARG G 29 *********************** 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 270 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.861 Fit side-chains REVERT: A 27 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: A 110 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6056 (pp20) REVERT: A 227 PHE cc_start: 0.7822 (t80) cc_final: 0.7480 (m-10) REVERT: A 228 ASN cc_start: 0.8615 (m-40) cc_final: 0.8112 (m110) REVERT: C 34 GLN cc_start: 0.6856 (tt0) cc_final: 0.6549 (pm20) REVERT: D 65 TRP cc_start: 0.7535 (m-10) cc_final: 0.6956 (t-100) REVERT: D 110 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6012 (pp20) REVERT: F 27 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: F 65 TRP cc_start: 0.7507 (OUTLIER) cc_final: 0.6931 (t-100) REVERT: F 100 SER cc_start: 0.8015 (m) cc_final: 0.7786 (m) REVERT: F 110 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5596 (pp20) REVERT: G 34 GLN cc_start: 0.6652 (tt0) cc_final: 0.6073 (pm20) REVERT: H 27 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: H 100 SER cc_start: 0.8125 (m) cc_final: 0.7897 (m) REVERT: H 110 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5406 (pp20) REVERT: H 228 ASN cc_start: 0.8059 (m-40) cc_final: 0.7573 (m110) outliers start: 49 outliers final: 36 residues processed: 255 average time/residue: 0.1896 time to fit residues: 68.1994 Evaluate side-chains 257 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 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 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 = 0.4053 r_free = 0.4053 target = 0.162488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110355 restraints weight = 13426.354| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.14 r_work: 0.3203 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9392 Z= 0.188 Angle : 0.667 10.561 12644 Z= 0.321 Chirality : 0.040 0.133 1424 Planarity : 0.003 0.024 1464 Dihedral : 18.078 119.276 1676 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.15 % Allowed : 30.57 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.27), residues: 1028 helix: 1.44 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.72 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 30 HIS 0.001 0.001 HIS D 22 PHE 0.015 0.001 PHE H 105 TYR 0.015 0.001 TYR A 57 ARG 0.004 0.000 ARG G 29 ********************** 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 265 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.998 Fit side-chains REVERT: A 27 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: A 81 LYS cc_start: 0.4666 (OUTLIER) cc_final: 0.4030 (tppt) REVERT: A 110 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5926 (pp20) REVERT: A 227 PHE cc_start: 0.7816 (t80) cc_final: 0.7454 (m-10) REVERT: A 228 ASN cc_start: 0.8606 (m-40) cc_final: 0.8156 (m110) REVERT: C 34 GLN cc_start: 0.6777 (tt0) cc_final: 0.6490 (pm20) REVERT: D 65 TRP cc_start: 0.7553 (OUTLIER) cc_final: 0.6957 (t-100) REVERT: D 81 LYS cc_start: 0.4636 (OUTLIER) cc_final: 0.4019 (tppt) REVERT: D 110 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5936 (pp20) REVERT: E 5 ILE cc_start: 0.6301 (mt) cc_final: 0.5714 (tp) REVERT: F 27 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: F 49 TYR cc_start: 0.8066 (t80) cc_final: 0.6876 (t80) REVERT: F 65 TRP cc_start: 0.7505 (m-10) cc_final: 0.6895 (t-100) REVERT: F 81 LYS cc_start: 0.4568 (OUTLIER) cc_final: 0.3919 (tppt) REVERT: F 110 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5570 (pp20) REVERT: G 34 GLN cc_start: 0.6543 (tt0) cc_final: 0.5999 (pm20) REVERT: H 27 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: H 65 TRP cc_start: 0.7553 (m-10) cc_final: 0.6990 (t-100) REVERT: H 100 SER cc_start: 0.8008 (m) cc_final: 0.7799 (m) REVERT: H 110 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5355 (pp20) REVERT: H 228 ASN cc_start: 0.8050 (m-40) cc_final: 0.7590 (m110) outliers start: 49 outliers final: 32 residues processed: 251 average time/residue: 0.1789 time to fit residues: 64.4233 Evaluate side-chains 255 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 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 213 LEU Chi-restraints excluded: chain D residue 229 LEU 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 180 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.162044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109943 restraints weight = 13163.867| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.11 r_work: 0.3193 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9392 Z= 0.204 Angle : 0.674 10.893 12644 Z= 0.324 Chirality : 0.041 0.130 1424 Planarity : 0.003 0.026 1464 Dihedral : 18.046 122.180 1676 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.88 % Allowed : 30.46 % Favored : 63.66 % 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: 0.83 (0.27), residues: 1028 helix: 1.45 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.73 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 30 HIS 0.001 0.001 HIS A 22 PHE 0.026 0.001 PHE H 105 TYR 0.013 0.001 TYR A 57 ARG 0.004 0.000 ARG I 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5711.31 seconds wall clock time: 100 minutes 38.83 seconds (6038.83 seconds total)