Starting phenix.real_space_refine on Sat Mar 16 07:51:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un8_26616/03_2024/7un8_26616_updated.pdb" } resolution = 3.3 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= 0.002 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 6 5.49 5 S 48 5.16 5 C 8986 2.51 5 N 2301 2.21 5 O 2726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 35": "OD1" <-> "OD2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ASP 287": "OD1" <-> "OD2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F ASP 130": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14067 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2324 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 3 Chain: "B" Number of atoms: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2324 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 3 Chain: "C" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2315 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 3 Chain: "D" Number of atoms: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2324 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 3 Chain: "E" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2318 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 3 Chain: "F" Number of atoms: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2324 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 3 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'C2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.36, per 1000 atoms: 0.52 Number of scatterers: 14067 At special positions: 0 Unit cell: (106.425, 78.375, 132.825, 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 6 15.00 O 2726 8.00 N 2301 7.00 C 8986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.29 Conformation dependent library (CDL) restraints added in 2.5 seconds 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 31 sheets defined 38.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.953A pdb=" N GLU A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 306 removed outlier: 3.691A pdb=" N GLY A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 23 removed outlier: 4.006A pdb=" N ASN B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.954A pdb=" N LEU B 271 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 305 Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.872A pdb=" N GLU C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 164 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 262 through 274 Processing helix chain 'C' and resid 284 through 306 removed outlier: 3.781A pdb=" N GLY C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 23 removed outlier: 3.978A pdb=" N ASN D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 131 through 145 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.963A pdb=" N LEU D 271 " --> pdb=" O VAL D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 305 Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.823A pdb=" N GLU E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 164 Processing helix chain 'E' and resid 166 through 176 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 284 through 306 removed outlier: 3.679A pdb=" N GLY E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 23 removed outlier: 3.980A pdb=" N ASN F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 166 through 176 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 262 through 274 removed outlier: 3.958A pdb=" N LEU F 271 " --> pdb=" O VAL F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 305 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.990A pdb=" N GLU A 29 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 7 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 31 " --> pdb=" O ILE A 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 57 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.681A pdb=" N LEU A 74 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 178 through 181 Processing sheet with id= E, first strand: chain 'A' and resid 257 through 259 Processing sheet with id= F, first strand: chain 'A' and resid 220 through 223 Processing sheet with id= G, first strand: chain 'B' and resid 3 through 7 Processing sheet with id= H, first strand: chain 'B' and resid 57 through 61 Processing sheet with id= I, first strand: chain 'B' and resid 178 through 181 Processing sheet with id= J, first strand: chain 'B' and resid 315 through 318 removed outlier: 8.206A pdb=" N ASN B 316 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL B 193 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU B 318 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 195 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 253 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE B 191 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 255 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL B 193 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 257 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL B 195 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP B 259 " --> pdb=" O VAL B 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 220 through 223 Processing sheet with id= L, first strand: chain 'C' and resid 4 through 7 removed outlier: 6.993A pdb=" N GLU C 29 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE C 7 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 31 " --> pdb=" O ILE C 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 57 through 61 Processing sheet with id= N, first strand: chain 'C' and resid 178 through 181 Processing sheet with id= O, first strand: chain 'C' and resid 257 through 259 Processing sheet with id= P, first strand: chain 'C' and resid 220 through 223 Processing sheet with id= Q, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= R, first strand: chain 'D' and resid 57 through 61 Processing sheet with id= S, first strand: chain 'D' and resid 178 through 181 Processing sheet with id= T, first strand: chain 'D' and resid 315 through 318 removed outlier: 8.138A pdb=" N ASN D 316 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 193 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU D 318 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 195 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL D 253 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE D 191 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE D 255 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL D 193 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU D 257 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL D 195 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP D 259 " --> pdb=" O VAL D 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 220 through 223 Processing sheet with id= V, first strand: chain 'E' and resid 4 through 7 removed outlier: 6.987A pdb=" N GLU E 29 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE E 7 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE E 31 " --> pdb=" O ILE E 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 57 through 61 Processing sheet with id= X, first strand: chain 'E' and resid 178 through 181 Processing sheet with id= Y, first strand: chain 'E' and resid 257 through 259 removed outlier: 3.590A pdb=" N ILE E 197 " --> pdb=" O LEU E 318 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 220 through 223 Processing sheet with id= AA, first strand: chain 'F' and resid 3 through 7 Processing sheet with id= AB, first strand: chain 'F' and resid 57 through 61 Processing sheet with id= AC, first strand: chain 'F' and resid 178 through 181 Processing sheet with id= AD, first strand: chain 'F' and resid 315 through 318 removed outlier: 8.255A pdb=" N ASN F 316 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 193 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU F 318 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL F 195 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 253 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE F 191 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE F 255 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL F 193 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 257 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL F 195 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP F 259 " --> pdb=" O VAL F 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'F' and resid 220 through 223 572 hydrogen bonds defined for protein. 1506 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: 3.89 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3095 1.33 - 1.45: 2813 1.45 - 1.57: 8306 1.57 - 1.69: 21 1.69 - 1.81: 66 Bond restraints: 14301 Sorted by residual: bond pdb=" C3A C2E E 401 " pdb=" C4A C2E E 401 " ideal model delta sigma weight residual 1.223 1.640 -0.417 2.00e-02 2.50e+03 4.35e+02 bond pdb=" C3A C2E B 401 " pdb=" C4A C2E B 401 " ideal model delta sigma weight residual 1.223 1.640 -0.417 2.00e-02 2.50e+03 4.35e+02 bond pdb=" C3A C2E D 401 " pdb=" C4A C2E D 401 " ideal model delta sigma weight residual 1.223 1.640 -0.417 2.00e-02 2.50e+03 4.34e+02 bond pdb=" C2A C2E B 401 " pdb=" C3A C2E B 401 " ideal model delta sigma weight residual 1.675 1.277 0.398 2.00e-02 2.50e+03 3.97e+02 bond pdb=" C2A C2E E 401 " pdb=" C3A C2E E 401 " ideal model delta sigma weight residual 1.675 1.277 0.398 2.00e-02 2.50e+03 3.96e+02 ... (remaining 14296 not shown) Histogram of bond angle deviations from ideal: 86.35 - 96.74: 1 96.74 - 107.13: 377 107.13 - 117.52: 10471 117.52 - 127.91: 8432 127.91 - 138.30: 85 Bond angle restraints: 19366 Sorted by residual: angle pdb=" C ASP D 26 " pdb=" N ASP D 27 " pdb=" CA ASP D 27 " ideal model delta sigma weight residual 122.61 138.30 -15.69 1.56e+00 4.11e-01 1.01e+02 angle pdb=" C1' C2E B 401 " pdb=" N9 C2E B 401 " pdb=" C4 C2E B 401 " ideal model delta sigma weight residual 152.55 125.03 27.52 3.00e+00 1.11e-01 8.42e+01 angle pdb=" C1' C2E B 401 " pdb=" N9 C2E B 401 " pdb=" C8 C2E B 401 " ideal model delta sigma weight residual 98.76 126.24 -27.48 3.00e+00 1.11e-01 8.39e+01 angle pdb=" C1' C2E D 401 " pdb=" N9 C2E D 401 " pdb=" C8 C2E D 401 " ideal model delta sigma weight residual 98.76 126.22 -27.46 3.00e+00 1.11e-01 8.38e+01 angle pdb=" C1' C2E D 401 " pdb=" N9 C2E D 401 " pdb=" C4 C2E D 401 " ideal model delta sigma weight residual 152.55 125.20 27.35 3.00e+00 1.11e-01 8.31e+01 ... (remaining 19361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.32: 8288 28.32 - 56.63: 313 56.63 - 84.94: 21 84.94 - 113.26: 11 113.26 - 141.57: 9 Dihedral angle restraints: 8642 sinusoidal: 3494 harmonic: 5148 Sorted by residual: dihedral pdb=" CD ARG C 192 " pdb=" NE ARG C 192 " pdb=" CZ ARG C 192 " pdb=" NH1 ARG C 192 " ideal model delta sinusoidal sigma weight residual 0.00 -52.75 52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " pdb=" CZ ARG A 192 " pdb=" NH1 ARG A 192 " ideal model delta sinusoidal sigma weight residual 0.00 -52.57 52.57 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CD ARG E 192 " pdb=" NE ARG E 192 " pdb=" CZ ARG E 192 " pdb=" NH1 ARG E 192 " ideal model delta sinusoidal sigma weight residual 0.00 -52.37 52.37 1 1.00e+01 1.00e-02 3.74e+01 ... (remaining 8639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.351: 2298 0.351 - 0.701: 1 0.701 - 1.052: 0 1.052 - 1.403: 1 1.403 - 1.753: 8 Chirality restraints: 2308 Sorted by residual: chirality pdb=" CG LEU F 140 " pdb=" CB LEU F 140 " pdb=" CD1 LEU F 140 " pdb=" CD2 LEU F 140 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.69e+01 chirality pdb=" CG LEU D 140 " pdb=" CB LEU D 140 " pdb=" CD1 LEU D 140 " pdb=" CD2 LEU D 140 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CG LEU B 24 " pdb=" CB LEU B 24 " pdb=" CD1 LEU B 24 " pdb=" CD2 LEU B 24 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.17e+01 ... (remaining 2305 not shown) Planarity restraints: 2409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " 0.706 9.50e-02 1.11e+02 3.18e-01 7.20e+01 pdb=" NE ARG C 192 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 192 " 0.694 9.50e-02 1.11e+02 3.13e-01 7.16e+01 pdb=" NE ARG E 192 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG E 192 " 0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG E 192 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG E 192 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " -0.687 9.50e-02 1.11e+02 3.10e-01 7.05e+01 pdb=" NE ARG A 192 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " -0.001 2.00e-02 2.50e+03 ... (remaining 2406 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 150 2.54 - 3.13: 11942 3.13 - 3.72: 22184 3.72 - 4.31: 32384 4.31 - 4.90: 52752 Nonbonded interactions: 119412 Sorted by model distance: nonbonded pdb=" OD2 ASP A 55 " pdb=" OH TYR A 288 " model vdw 1.944 2.440 nonbonded pdb=" OD2 ASP E 55 " pdb=" OH TYR E 288 " model vdw 1.985 2.440 nonbonded pdb=" OD2 ASP C 55 " pdb=" OH TYR C 288 " model vdw 2.016 2.440 nonbonded pdb=" OE2 GLU A 95 " pdb=" NE2 GLN C 279 " model vdw 2.025 2.520 nonbonded pdb=" OD2 ASP C 79 " pdb=" NZ LYS D 76 " model vdw 2.043 2.520 ... (remaining 119407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 68 or resid 74 through 322)) selection = (chain 'B' and (resid 2 through 68 or resid 74 through 322)) selection = (chain 'C' and (resid 2 through 68 or resid 74 through 322)) selection = (chain 'D' and (resid 2 through 68 or resid 74 through 322)) selection = (chain 'E' and (resid 2 through 68 or resid 74 through 322)) selection = (chain 'F' and (resid 2 through 68 or resid 74 through 322)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.020 Extract box with map and model: 7.090 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 37.800 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.014 0.417 14301 Z= 0.893 Angle : 0.993 27.524 19366 Z= 0.460 Chirality : 0.110 1.753 2308 Planarity : 0.015 0.318 2409 Dihedral : 15.815 141.575 5310 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.29 % Favored : 93.53 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.04 % Cbeta Deviations : 0.06 % 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: -1.88 (0.19), residues: 1732 helix: -0.00 (0.18), residues: 725 sheet: -2.54 (0.27), residues: 286 loop : -1.91 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 33 HIS 0.006 0.002 HIS C 256 PHE 0.018 0.002 PHE C 191 TYR 0.023 0.002 TYR D 303 ARG 0.061 0.005 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8196 (tm-30) REVERT: B 29 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7478 (mt-10) REVERT: B 303 TYR cc_start: 0.8354 (t80) cc_final: 0.8043 (t80) REVERT: D 168 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7537 (mmm-85) REVERT: D 287 ASP cc_start: 0.7746 (m-30) cc_final: 0.7393 (m-30) REVERT: E 50 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8147 (mm-40) REVERT: E 109 THR cc_start: 0.7531 (p) cc_final: 0.7220 (t) REVERT: E 282 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7448 (tm-30) REVERT: F 148 GLN cc_start: 0.8365 (pt0) cc_final: 0.7830 (pt0) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.3200 time to fit residues: 121.2725 Evaluate side-chains 176 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS B 139 HIS ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS C 174 HIS C 208 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN F 214 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14301 Z= 0.254 Angle : 0.614 8.761 19366 Z= 0.306 Chirality : 0.044 0.222 2308 Planarity : 0.004 0.061 2409 Dihedral : 12.449 139.909 1924 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.66 % Allowed : 8.73 % Favored : 89.62 % 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: -0.98 (0.20), residues: 1732 helix: 0.82 (0.19), residues: 741 sheet: -2.32 (0.26), residues: 312 loop : -1.37 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 33 HIS 0.006 0.001 HIS C 256 PHE 0.012 0.002 PHE C 238 TYR 0.017 0.002 TYR E 56 ARG 0.007 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.3035 (pttt) cc_final: 0.2371 (mtmt) REVERT: B 303 TYR cc_start: 0.8344 (t80) cc_final: 0.8139 (t80) REVERT: C 15 THR cc_start: 0.7312 (p) cc_final: 0.7013 (t) REVERT: D 4 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7500 (mtt90) REVERT: D 68 LYS cc_start: 0.6714 (tppt) cc_final: 0.6507 (mppt) REVERT: D 75 THR cc_start: 0.7550 (t) cc_final: 0.7330 (m) REVERT: D 168 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7644 (mmm-85) REVERT: E 109 THR cc_start: 0.8229 (p) cc_final: 0.8012 (t) REVERT: E 168 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.7273 (mtp180) REVERT: E 169 VAL cc_start: 0.8508 (p) cc_final: 0.8283 (p) REVERT: E 204 ASN cc_start: 0.7481 (t0) cc_final: 0.7136 (t0) REVERT: E 282 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7667 (tm-30) REVERT: F 291 MET cc_start: 0.7518 (tmm) cc_final: 0.7260 (tmm) REVERT: F 295 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7089 (mm-30) outliers start: 26 outliers final: 13 residues processed: 257 average time/residue: 0.3208 time to fit residues: 112.8320 Evaluate side-chains 195 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 279 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 0.0980 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.0060 chunk 53 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS E 139 HIS E 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14301 Z= 0.175 Angle : 0.548 11.309 19366 Z= 0.269 Chirality : 0.042 0.277 2308 Planarity : 0.004 0.048 2409 Dihedral : 11.701 124.048 1924 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.17 % Allowed : 12.80 % Favored : 85.03 % 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: -0.46 (0.20), residues: 1732 helix: 1.23 (0.19), residues: 734 sheet: -1.87 (0.25), residues: 329 loop : -1.12 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 33 HIS 0.002 0.001 HIS A 239 PHE 0.014 0.001 PHE F 209 TYR 0.012 0.001 TYR F 314 ARG 0.008 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.2813 (pttt) cc_final: 0.2165 (mtmt) REVERT: B 131 LYS cc_start: 0.4318 (pttt) cc_final: 0.3863 (pttt) REVERT: C 15 THR cc_start: 0.7364 (p) cc_final: 0.7026 (t) REVERT: D 4 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7432 (mtt90) REVERT: D 13 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8041 (mm-40) REVERT: D 75 THR cc_start: 0.7527 (t) cc_final: 0.7265 (m) REVERT: E 76 LYS cc_start: 0.6790 (ptpt) cc_final: 0.6465 (mtmt) REVERT: E 95 GLU cc_start: 0.7381 (pm20) cc_final: 0.6886 (mm-30) REVERT: E 137 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7415 (ttp80) REVERT: E 168 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7393 (tpt90) REVERT: E 282 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7688 (tm-30) REVERT: F 57 SER cc_start: 0.8578 (p) cc_final: 0.8269 (p) outliers start: 34 outliers final: 18 residues processed: 241 average time/residue: 0.3267 time to fit residues: 107.9676 Evaluate side-chains 190 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 271 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 0.0870 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN B 204 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN D 50 GLN E 139 HIS E 279 GLN F 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14301 Z= 0.217 Angle : 0.563 11.337 19366 Z= 0.273 Chirality : 0.042 0.261 2308 Planarity : 0.004 0.045 2409 Dihedral : 11.360 120.993 1924 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.87 % Allowed : 13.44 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1732 helix: 1.41 (0.19), residues: 732 sheet: -1.76 (0.26), residues: 329 loop : -1.01 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 33 HIS 0.029 0.001 HIS C 256 PHE 0.012 0.001 PHE F 236 TYR 0.009 0.001 TYR F 314 ARG 0.006 0.001 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.2845 (pttt) cc_final: 0.2170 (mtmt) REVERT: B 277 SER cc_start: 0.7887 (t) cc_final: 0.7658 (p) REVERT: C 137 ARG cc_start: 0.7005 (ttp80) cc_final: 0.6690 (ptt90) REVERT: D 4 ARG cc_start: 0.7783 (ttm110) cc_final: 0.7503 (mtt90) REVERT: D 13 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8078 (mm-40) REVERT: D 307 ARG cc_start: 0.7772 (mmp-170) cc_final: 0.7539 (mmm-85) REVERT: E 95 GLU cc_start: 0.7222 (pm20) cc_final: 0.6795 (mm-30) REVERT: E 168 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7493 (tpt90) REVERT: F 57 SER cc_start: 0.8610 (p) cc_final: 0.8261 (p) REVERT: F 75 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7709 (p) REVERT: F 291 MET cc_start: 0.7547 (tmm) cc_final: 0.7277 (tmm) outliers start: 45 outliers final: 25 residues processed: 243 average time/residue: 0.3168 time to fit residues: 105.9061 Evaluate side-chains 196 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 202 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 143 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS D 50 GLN E 139 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS E 279 GLN F 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14301 Z= 0.176 Angle : 0.536 10.156 19366 Z= 0.262 Chirality : 0.041 0.263 2308 Planarity : 0.003 0.044 2409 Dihedral : 10.996 119.535 1924 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.23 % Allowed : 15.16 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.20), residues: 1732 helix: 1.56 (0.19), residues: 733 sheet: -1.61 (0.26), residues: 329 loop : -0.91 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 33 HIS 0.002 0.001 HIS C 256 PHE 0.010 0.001 PHE E 297 TYR 0.010 0.001 TYR F 303 ARG 0.006 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.2868 (pttt) cc_final: 0.2208 (mtmt) REVERT: B 187 LYS cc_start: 0.6208 (mmtm) cc_final: 0.5786 (tttp) REVERT: B 277 SER cc_start: 0.7878 (t) cc_final: 0.7670 (p) REVERT: C 137 ARG cc_start: 0.7069 (ttp80) cc_final: 0.6759 (ptt90) REVERT: C 142 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8252 (mttm) REVERT: E 95 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6782 (mm-30) REVERT: E 137 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7595 (ttp80) REVERT: F 57 SER cc_start: 0.8596 (p) cc_final: 0.8265 (p) outliers start: 35 outliers final: 26 residues processed: 231 average time/residue: 0.3243 time to fit residues: 102.4779 Evaluate side-chains 202 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 256 HIS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 253 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 0.0270 chunk 41 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS F 256 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14301 Z= 0.214 Angle : 0.554 11.393 19366 Z= 0.269 Chirality : 0.042 0.268 2308 Planarity : 0.004 0.049 2409 Dihedral : 10.899 119.884 1924 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.87 % Allowed : 15.48 % Favored : 81.66 % 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: 0.03 (0.20), residues: 1732 helix: 1.58 (0.19), residues: 737 sheet: -1.49 (0.26), residues: 340 loop : -0.87 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 33 HIS 0.011 0.001 HIS E 256 PHE 0.009 0.001 PHE B 88 TYR 0.009 0.001 TYR D 303 ARG 0.006 0.001 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.2979 (pttt) cc_final: 0.2313 (mtmt) REVERT: A 146 MET cc_start: 0.8030 (mmt) cc_final: 0.7671 (mmt) REVERT: B 187 LYS cc_start: 0.6371 (mmtm) cc_final: 0.6001 (tttp) REVERT: B 277 SER cc_start: 0.8002 (t) cc_final: 0.7771 (p) REVERT: C 137 ARG cc_start: 0.7125 (ttp80) cc_final: 0.6744 (ptt90) REVERT: C 142 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8223 (mttm) REVERT: E 95 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6776 (mm-30) REVERT: F 57 SER cc_start: 0.8615 (p) cc_final: 0.8293 (p) REVERT: F 291 MET cc_start: 0.7486 (tmm) cc_final: 0.7267 (tmm) outliers start: 45 outliers final: 34 residues processed: 229 average time/residue: 0.3105 time to fit residues: 98.7356 Evaluate side-chains 207 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 279 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 139 HIS E 256 HIS E 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14301 Z= 0.281 Angle : 0.599 11.863 19366 Z= 0.290 Chirality : 0.043 0.275 2308 Planarity : 0.004 0.042 2409 Dihedral : 11.122 120.150 1924 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.44 % Allowed : 15.41 % Favored : 81.15 % 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: -0.04 (0.20), residues: 1732 helix: 1.43 (0.19), residues: 738 sheet: -1.40 (0.27), residues: 333 loop : -0.87 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 33 HIS 0.003 0.001 HIS A 139 PHE 0.012 0.001 PHE B 88 TYR 0.012 0.001 TYR C 217 ARG 0.007 0.001 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 184 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.2993 (pttt) cc_final: 0.2330 (mtmt) REVERT: A 146 MET cc_start: 0.8038 (mmt) cc_final: 0.7669 (mmt) REVERT: B 187 LYS cc_start: 0.6585 (mmtm) cc_final: 0.6236 (tttp) REVERT: B 277 SER cc_start: 0.8146 (t) cc_final: 0.7899 (p) REVERT: C 137 ARG cc_start: 0.7141 (ttp80) cc_final: 0.6726 (ptt90) REVERT: C 142 LYS cc_start: 0.8519 (mmtp) cc_final: 0.8280 (mttm) REVERT: C 192 ARG cc_start: 0.7578 (tmm160) cc_final: 0.7363 (tmm160) REVERT: D 68 LYS cc_start: 0.5325 (tptt) cc_final: 0.4919 (tptt) REVERT: E 95 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6814 (mm-30) REVERT: F 24 LEU cc_start: 0.8338 (pp) cc_final: 0.8086 (pp) REVERT: F 57 SER cc_start: 0.8645 (p) cc_final: 0.8302 (p) outliers start: 54 outliers final: 41 residues processed: 230 average time/residue: 0.3090 time to fit residues: 98.6272 Evaluate side-chains 212 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 279 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 69 GLN E 139 HIS E 256 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14301 Z= 0.285 Angle : 0.606 13.192 19366 Z= 0.295 Chirality : 0.043 0.275 2308 Planarity : 0.004 0.042 2409 Dihedral : 11.223 118.391 1924 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.12 % Allowed : 16.50 % Favored : 80.38 % 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: -0.16 (0.20), residues: 1732 helix: 1.27 (0.19), residues: 743 sheet: -1.45 (0.27), residues: 334 loop : -0.87 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 33 HIS 0.003 0.001 HIS A 139 PHE 0.011 0.001 PHE B 88 TYR 0.012 0.001 TYR C 217 ARG 0.010 0.001 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.2827 (pttt) cc_final: 0.2189 (mtmt) REVERT: A 187 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7253 (mptt) REVERT: B 187 LYS cc_start: 0.6726 (mmtm) cc_final: 0.6360 (tttp) REVERT: B 277 SER cc_start: 0.8364 (t) cc_final: 0.8037 (p) REVERT: C 14 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7199 (mm) REVERT: C 56 TYR cc_start: 0.8306 (m-80) cc_final: 0.7447 (m-80) REVERT: C 137 ARG cc_start: 0.7140 (ttp80) cc_final: 0.6675 (ptt90) REVERT: C 142 LYS cc_start: 0.8547 (mmtp) cc_final: 0.8343 (mttm) REVERT: D 68 LYS cc_start: 0.5211 (tptt) cc_final: 0.4581 (tptt) REVERT: E 95 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: F 24 LEU cc_start: 0.8360 (pp) cc_final: 0.8135 (pp) REVERT: F 57 SER cc_start: 0.8637 (p) cc_final: 0.8298 (p) outliers start: 49 outliers final: 42 residues processed: 228 average time/residue: 0.3281 time to fit residues: 103.9365 Evaluate side-chains 210 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 223 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0670 chunk 160 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 ASN E 50 GLN E 139 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 14301 Z= 0.440 Angle : 0.706 13.562 19366 Z= 0.346 Chirality : 0.046 0.294 2308 Planarity : 0.004 0.048 2409 Dihedral : 11.819 135.572 1924 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.57 % Allowed : 16.69 % Favored : 79.75 % 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: -0.53 (0.19), residues: 1732 helix: 0.87 (0.18), residues: 741 sheet: -1.45 (0.27), residues: 325 loop : -1.07 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 33 HIS 0.008 0.001 HIS C 256 PHE 0.017 0.002 PHE B 88 TYR 0.019 0.002 TYR C 217 ARG 0.009 0.001 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 177 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.3065 (pttt) cc_final: 0.2421 (mtmt) REVERT: A 187 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7449 (mptt) REVERT: B 187 LYS cc_start: 0.6843 (mmtm) cc_final: 0.6505 (tttp) REVERT: C 56 TYR cc_start: 0.8419 (m-80) cc_final: 0.7484 (m-80) REVERT: C 142 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8374 (mttm) REVERT: C 146 MET cc_start: 0.7709 (mmt) cc_final: 0.7220 (mmt) REVERT: E 95 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: F 33 TRP cc_start: 0.8136 (p-90) cc_final: 0.7706 (p-90) REVERT: F 57 SER cc_start: 0.8658 (p) cc_final: 0.8330 (p) REVERT: F 182 GLU cc_start: 0.6317 (mm-30) cc_final: 0.6063 (tm-30) REVERT: F 291 MET cc_start: 0.7519 (tmm) cc_final: 0.7093 (tmm) outliers start: 56 outliers final: 43 residues processed: 223 average time/residue: 0.3298 time to fit residues: 100.4949 Evaluate side-chains 213 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 279 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 114 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS E 50 GLN E 139 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14301 Z= 0.193 Angle : 0.585 11.857 19366 Z= 0.286 Chirality : 0.043 0.302 2308 Planarity : 0.004 0.047 2409 Dihedral : 11.261 116.140 1924 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.55 % Allowed : 18.22 % Favored : 79.24 % 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: -0.22 (0.20), residues: 1732 helix: 1.19 (0.19), residues: 743 sheet: -1.43 (0.27), residues: 330 loop : -0.89 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 33 HIS 0.005 0.001 HIS C 256 PHE 0.012 0.001 PHE A 297 TYR 0.016 0.001 TYR E 314 ARG 0.010 0.001 ARG F 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.6922 (m-30) cc_final: 0.6674 (m-30) REVERT: A 131 LYS cc_start: 0.3043 (pttt) cc_final: 0.2353 (mtmt) REVERT: A 146 MET cc_start: 0.8069 (mmt) cc_final: 0.7837 (mmt) REVERT: A 187 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7288 (mptt) REVERT: B 187 LYS cc_start: 0.6771 (mmtm) cc_final: 0.6434 (tttp) REVERT: C 56 TYR cc_start: 0.8266 (m-80) cc_final: 0.7392 (m-80) REVERT: C 137 ARG cc_start: 0.7137 (ttp80) cc_final: 0.6700 (ptt90) REVERT: C 146 MET cc_start: 0.7508 (mmt) cc_final: 0.7044 (mmt) REVERT: D 68 LYS cc_start: 0.5228 (tptt) cc_final: 0.4600 (tptt) REVERT: E 95 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: E 169 VAL cc_start: 0.8416 (p) cc_final: 0.8199 (p) REVERT: E 190 SER cc_start: 0.7254 (t) cc_final: 0.6730 (m) REVERT: F 57 SER cc_start: 0.8556 (p) cc_final: 0.8219 (p) outliers start: 40 outliers final: 36 residues processed: 221 average time/residue: 0.3177 time to fit residues: 96.6029 Evaluate side-chains 209 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 256 HIS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 223 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 20 optimal weight: 0.4980 chunk 38 optimal weight: 0.3980 chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS E 50 GLN E 139 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.128827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108686 restraints weight = 22700.288| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.06 r_work: 0.3338 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14301 Z= 0.214 Angle : 0.590 11.374 19366 Z= 0.288 Chirality : 0.043 0.275 2308 Planarity : 0.004 0.046 2409 Dihedral : 11.036 113.610 1924 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.80 % Allowed : 18.41 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.20), residues: 1732 helix: 1.25 (0.19), residues: 743 sheet: -1.37 (0.28), residues: 325 loop : -0.84 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 33 HIS 0.010 0.001 HIS E 256 PHE 0.010 0.001 PHE A 297 TYR 0.015 0.001 TYR E 314 ARG 0.009 0.001 ARG F 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.79 seconds wall clock time: 58 minutes 33.14 seconds (3513.14 seconds total)