Starting phenix.real_space_refine on Fri Jul 19 21:07:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/07_2024/8xzj_38798.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/07_2024/8xzj_38798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/07_2024/8xzj_38798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/07_2024/8xzj_38798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/07_2024/8xzj_38798.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/07_2024/8xzj_38798.cif" } resolution = 3.0 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= 0.002 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 5804 2.51 5 N 1536 2.21 5 O 1693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 313": "OD1" <-> "OD2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9106 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2410 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 112 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.28, per 1000 atoms: 0.58 Number of scatterers: 9106 At special positions: 0 Unit cell: (100.44, 132.06, 114.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1693 8.00 N 1536 7.00 C 5804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.16 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.11 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 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: 3.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 39.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'R' and resid 26 through 55 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 78 Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.848A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 132 removed outlier: 4.346A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.855A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.843A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 216 removed outlier: 3.705A pdb=" N THR R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 232 removed outlier: 3.697A pdb=" N GLY R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 274 Proline residue: R 263 - end of helix removed outlier: 4.199A pdb=" N THR R 269 " --> pdb=" O HIS R 265 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU R 270 " --> pdb=" O LEU R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 311 Proline residue: R 292 - end of helix removed outlier: 3.728A pdb=" N SER R 298 " --> pdb=" O CYS R 294 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR R 299 " --> pdb=" O THR R 295 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL R 300 " --> pdb=" O CYS R 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix removed outlier: 3.704A pdb=" N ALA R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.520A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.023A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.231A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.207A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.873A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.137A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.451A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.623A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.542A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.839A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.278A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.610A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.515A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.621A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.991A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.991A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.427A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.055A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1272 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: 2.65 Time building geometry restraints manager: 3.78 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: 2196 1.33 - 1.45: 1991 1.45 - 1.57: 5015 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 9307 Sorted by residual: bond pdb=" N ARG L 2 " pdb=" CA ARG L 2 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.24e+01 bond pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 1.474 1.428 0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" N VAL R 79 " pdb=" CA VAL R 79 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.09e-02 8.42e+03 1.05e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" C4A NAL L 11 " pdb=" C8A NAL L 11 " ideal model delta sigma weight residual 1.419 1.480 -0.061 2.00e-02 2.50e+03 9.34e+00 ... (remaining 9302 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.13: 265 107.13 - 113.93: 5184 113.93 - 120.74: 4070 120.74 - 127.54: 3002 127.54 - 134.34: 92 Bond angle restraints: 12613 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.23 103.54 9.69 1.24e+00 6.50e-01 6.11e+01 angle pdb=" C ASP R 313 " pdb=" N PRO R 314 " pdb=" CA PRO R 314 " ideal model delta sigma weight residual 119.32 126.59 -7.27 1.14e+00 7.69e-01 4.07e+01 angle pdb=" N LEU R 266 " pdb=" CA LEU R 266 " pdb=" C LEU R 266 " ideal model delta sigma weight residual 113.97 107.43 6.54 1.28e+00 6.10e-01 2.61e+01 angle pdb=" N GLN R 226 " pdb=" CA GLN R 226 " pdb=" C GLN R 226 " ideal model delta sigma weight residual 113.97 107.48 6.49 1.28e+00 6.10e-01 2.57e+01 angle pdb=" N LEU R 308 " pdb=" CA LEU R 308 " pdb=" C LEU R 308 " ideal model delta sigma weight residual 111.36 116.79 -5.43 1.09e+00 8.42e-01 2.48e+01 ... (remaining 12608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 5235 17.12 - 34.24: 178 34.24 - 51.35: 61 51.35 - 68.47: 19 68.47 - 85.59: 6 Dihedral angle restraints: 5499 sinusoidal: 2130 harmonic: 3369 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 176.96 -83.96 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CD ARG R 91 " pdb=" NE ARG R 91 " pdb=" CZ ARG R 91 " pdb=" NH1 ARG R 91 " ideal model delta sinusoidal sigma weight residual 0.00 -41.70 41.70 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 916 0.047 - 0.094: 303 0.094 - 0.141: 135 0.141 - 0.188: 58 0.188 - 0.235: 12 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL R 300 " pdb=" N VAL R 300 " pdb=" C VAL R 300 " pdb=" CB VAL R 300 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1421 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 91 " 0.723 9.50e-02 1.11e+02 3.24e-01 6.39e+01 pdb=" NE ARG R 91 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG R 91 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG R 91 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 91 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 8 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C LYS L 8 " -0.078 2.00e-02 2.50e+03 pdb=" O LYS L 8 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY L 9 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.59e+00 pdb=" C GLN B 75 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.018 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1984 2.78 - 3.31: 8657 3.31 - 3.84: 15376 3.84 - 4.37: 19249 4.37 - 4.90: 32319 Nonbonded interactions: 77585 Sorted by model distance: nonbonded pdb=" CD1 ILE R 68 " pdb=" O TYR R 309 " model vdw 2.252 3.460 nonbonded pdb=" O PRO R 280 " pdb=" N ASP R 282 " model vdw 2.272 2.520 nonbonded pdb=" OD1 ASP R 23 " pdb=" NZ LYS L 8 " model vdw 2.287 2.520 nonbonded pdb=" OD2 ASP R 75 " pdb=" ND2 ASN R 305 " model vdw 2.330 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 2.440 ... (remaining 77580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 0.061 9307 Z= 0.690 Angle : 0.945 9.693 12613 Z= 0.660 Chirality : 0.064 0.235 1424 Planarity : 0.010 0.324 1588 Dihedral : 11.329 85.590 3312 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.84 % Favored : 97.89 % Rotamer: Outliers : 2.72 % Allowed : 2.32 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.36 (0.24), residues: 1139 helix: 0.19 (0.24), residues: 400 sheet: 0.82 (0.29), residues: 288 loop : 0.09 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 95 HIS 0.009 0.001 HIS B 91 PHE 0.024 0.001 PHE B 199 TYR 0.034 0.002 TYR B 105 ARG 0.013 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: R 78 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7687 (t80) REVERT: R 293 TYR cc_start: 0.6553 (m-80) cc_final: 0.6161 (m-80) REVERT: A 32 ARG cc_start: 0.7145 (mtm-85) cc_final: 0.6692 (mtm180) REVERT: A 186 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6221 (mt-10) REVERT: B 156 GLN cc_start: 0.8012 (mt0) cc_final: 0.7779 (mt0) REVERT: B 176 GLN cc_start: 0.8320 (mt0) cc_final: 0.8024 (mt0) REVERT: B 219 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6774 (mtm110) REVERT: B 294 CYS cc_start: 0.7664 (m) cc_final: 0.7318 (m) REVERT: B 325 MET cc_start: 0.8126 (mmt) cc_final: 0.7790 (mmm) REVERT: G 59 ASN cc_start: 0.7839 (t0) cc_final: 0.7583 (t0) REVERT: S 23 SER cc_start: 0.8030 (t) cc_final: 0.7778 (m) REVERT: S 85 SER cc_start: 0.8182 (m) cc_final: 0.7971 (p) REVERT: S 87 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6829 (mtt-85) REVERT: L 8 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6644 (pttm) outliers start: 27 outliers final: 8 residues processed: 240 average time/residue: 1.2510 time to fit residues: 319.1026 Evaluate side-chains 143 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 91 HIS B 293 ASN S 39 GLN S 130 GLN S 159 ASN S 167 GLN S 182 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9307 Z= 0.210 Angle : 0.569 7.804 12613 Z= 0.303 Chirality : 0.042 0.147 1424 Planarity : 0.004 0.048 1588 Dihedral : 6.140 59.491 1281 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.76 % Favored : 98.07 % Rotamer: Outliers : 3.43 % Allowed : 10.99 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.17 (0.25), residues: 1139 helix: 1.54 (0.26), residues: 410 sheet: 0.79 (0.31), residues: 264 loop : 0.20 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS G 44 PHE 0.024 0.002 PHE R 110 TYR 0.014 0.002 TYR R 114 ARG 0.008 0.001 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 1.043 Fit side-chains REVERT: R 41 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6537 (mt) REVERT: R 162 MET cc_start: 0.6928 (ptt) cc_final: 0.6675 (ptt) REVERT: R 272 MET cc_start: 0.6192 (mtm) cc_final: 0.5685 (ptt) REVERT: R 293 TYR cc_start: 0.6640 (m-80) cc_final: 0.6394 (m-80) REVERT: A 198 MET cc_start: 0.7730 (ttm) cc_final: 0.7525 (ttp) REVERT: A 253 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8010 (mm) REVERT: A 274 PHE cc_start: 0.7050 (t80) cc_final: 0.6603 (t80) REVERT: B 19 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6464 (tpp-160) REVERT: B 212 ASP cc_start: 0.7743 (t0) cc_final: 0.7469 (t0) REVERT: B 217 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7952 (pmt) REVERT: B 219 ARG cc_start: 0.7015 (mtt-85) cc_final: 0.6739 (mtm110) REVERT: B 254 ASP cc_start: 0.6767 (t70) cc_final: 0.6513 (t0) REVERT: B 325 MET cc_start: 0.8083 (mmt) cc_final: 0.7520 (mmm) REVERT: G 59 ASN cc_start: 0.7699 (t0) cc_final: 0.7434 (t0) REVERT: S 23 SER cc_start: 0.8127 (t) cc_final: 0.7898 (m) REVERT: S 85 SER cc_start: 0.8197 (m) cc_final: 0.7842 (p) REVERT: S 87 ARG cc_start: 0.6987 (mtt180) cc_final: 0.6671 (mtt90) outliers start: 34 outliers final: 12 residues processed: 168 average time/residue: 1.2682 time to fit residues: 227.2673 Evaluate side-chains 142 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 ASN R 180 GLN A 311 ASN A 333 GLN B 32 GLN B 75 GLN B 293 ASN S 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9307 Z= 0.274 Angle : 0.584 8.268 12613 Z= 0.306 Chirality : 0.043 0.148 1424 Planarity : 0.004 0.051 1588 Dihedral : 5.267 51.507 1266 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.28 % Favored : 97.63 % Rotamer: Outliers : 3.63 % Allowed : 12.20 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.24 (0.25), residues: 1139 helix: 1.84 (0.26), residues: 403 sheet: 0.73 (0.30), residues: 268 loop : 0.08 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.030 0.002 PHE R 110 TYR 0.010 0.002 TYR R 35 ARG 0.006 0.000 ARG R 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: R 36 MET cc_start: 0.6154 (tpp) cc_final: 0.3553 (tmm) REVERT: R 162 MET cc_start: 0.6774 (ptt) cc_final: 0.6453 (ptt) REVERT: R 268 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.7043 (ttmm) REVERT: R 272 MET cc_start: 0.6248 (mtm) cc_final: 0.5815 (ptt) REVERT: R 287 LEU cc_start: 0.8072 (mp) cc_final: 0.7736 (tt) REVERT: A 46 LYS cc_start: 0.6738 (mtmm) cc_final: 0.6433 (mtpm) REVERT: A 184 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7625 (tt) REVERT: A 198 MET cc_start: 0.7800 (ttm) cc_final: 0.7596 (ttp) REVERT: A 270 LYS cc_start: 0.7358 (mttt) cc_final: 0.6943 (mmpt) REVERT: A 274 PHE cc_start: 0.7036 (t80) cc_final: 0.6692 (t80) REVERT: B 19 ARG cc_start: 0.7281 (ttp-110) cc_final: 0.6443 (tpp-160) REVERT: B 57 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8468 (mttt) REVERT: B 217 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7963 (pmt) REVERT: B 219 ARG cc_start: 0.7024 (mtt-85) cc_final: 0.6746 (mtm110) REVERT: B 237 ASN cc_start: 0.7574 (p0) cc_final: 0.7372 (p0) REVERT: B 254 ASP cc_start: 0.6744 (t70) cc_final: 0.6499 (t0) REVERT: B 325 MET cc_start: 0.7986 (mmt) cc_final: 0.7726 (mmm) REVERT: G 59 ASN cc_start: 0.7720 (t0) cc_final: 0.7486 (t0) REVERT: S 6 GLU cc_start: 0.7927 (mp0) cc_final: 0.7541 (mp0) REVERT: S 23 SER cc_start: 0.8215 (t) cc_final: 0.7956 (m) REVERT: S 85 SER cc_start: 0.8194 (m) cc_final: 0.7788 (p) REVERT: S 87 ARG cc_start: 0.6910 (mtt180) cc_final: 0.6590 (mtt90) outliers start: 36 outliers final: 14 residues processed: 159 average time/residue: 1.2096 time to fit residues: 205.3696 Evaluate side-chains 150 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 268 LYS Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN B 293 ASN S 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9307 Z= 0.224 Angle : 0.538 7.711 12613 Z= 0.284 Chirality : 0.041 0.142 1424 Planarity : 0.004 0.053 1588 Dihedral : 5.004 57.476 1266 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.81 % Rotamer: Outliers : 3.43 % Allowed : 13.51 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.23 (0.26), residues: 1139 helix: 1.83 (0.27), residues: 407 sheet: 0.69 (0.30), residues: 269 loop : 0.06 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.025 0.002 PHE R 110 TYR 0.017 0.002 TYR R 93 ARG 0.005 0.000 ARG R 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.992 Fit side-chains REVERT: R 162 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6432 (ptt) REVERT: R 182 TYR cc_start: 0.6572 (p90) cc_final: 0.6332 (p90) REVERT: R 272 MET cc_start: 0.6291 (mtm) cc_final: 0.5889 (ptt) REVERT: A 21 ARG cc_start: 0.7647 (ttp-110) cc_final: 0.7438 (ttm110) REVERT: A 184 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7665 (tp) REVERT: A 198 MET cc_start: 0.7796 (ttm) cc_final: 0.7586 (ttp) REVERT: A 270 LYS cc_start: 0.7434 (mttt) cc_final: 0.7189 (mmtm) REVERT: A 274 PHE cc_start: 0.7114 (t80) cc_final: 0.6752 (t80) REVERT: B 57 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8416 (mttt) REVERT: B 177 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 217 MET cc_start: 0.8334 (pmm) cc_final: 0.7948 (pmt) REVERT: B 219 ARG cc_start: 0.7042 (mtt-85) cc_final: 0.6750 (mtm110) REVERT: B 254 ASP cc_start: 0.6707 (t70) cc_final: 0.6466 (t0) REVERT: B 322 ASP cc_start: 0.7865 (m-30) cc_final: 0.7649 (m-30) REVERT: B 325 MET cc_start: 0.7834 (mmt) cc_final: 0.7557 (mmm) REVERT: G 59 ASN cc_start: 0.7681 (t0) cc_final: 0.7471 (t0) REVERT: S 23 SER cc_start: 0.8147 (t) cc_final: 0.7911 (m) REVERT: S 85 SER cc_start: 0.8171 (m) cc_final: 0.7786 (p) REVERT: S 87 ARG cc_start: 0.6874 (mtt180) cc_final: 0.6567 (mtt90) REVERT: S 201 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7858 (t) outliers start: 34 outliers final: 12 residues processed: 157 average time/residue: 1.2989 time to fit residues: 217.2384 Evaluate side-chains 140 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 176 GLN B 293 ASN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9307 Z= 0.341 Angle : 0.606 9.123 12613 Z= 0.318 Chirality : 0.044 0.149 1424 Planarity : 0.004 0.053 1588 Dihedral : 4.746 27.475 1260 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.93 % Rotamer: Outliers : 3.63 % Allowed : 14.82 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.95 (0.26), residues: 1139 helix: 1.57 (0.27), residues: 407 sheet: 0.53 (0.31), residues: 268 loop : -0.04 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS G 44 PHE 0.025 0.002 PHE R 110 TYR 0.023 0.002 TYR R 93 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 0.955 Fit side-chains REVERT: R 139 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.6707 (pmt-80) REVERT: R 162 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6391 (ptt) REVERT: R 272 MET cc_start: 0.6382 (mtm) cc_final: 0.6083 (ttp) REVERT: A 184 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 198 MET cc_start: 0.7831 (ttm) cc_final: 0.7577 (ttp) REVERT: A 270 LYS cc_start: 0.7424 (mttt) cc_final: 0.7024 (mmpt) REVERT: A 274 PHE cc_start: 0.7248 (t80) cc_final: 0.6909 (t80) REVERT: B 57 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8509 (mttt) REVERT: B 214 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6073 (mmt180) REVERT: B 217 MET cc_start: 0.8231 (pmm) cc_final: 0.7858 (pmt) REVERT: B 219 ARG cc_start: 0.7098 (mtt-85) cc_final: 0.6780 (mtm110) REVERT: B 254 ASP cc_start: 0.6723 (t70) cc_final: 0.6484 (t0) REVERT: B 322 ASP cc_start: 0.7924 (m-30) cc_final: 0.7718 (m-30) REVERT: G 59 ASN cc_start: 0.7705 (t0) cc_final: 0.7479 (t0) REVERT: S 6 GLU cc_start: 0.7861 (mp0) cc_final: 0.7569 (mt-10) REVERT: S 23 SER cc_start: 0.8175 (t) cc_final: 0.7920 (m) REVERT: S 85 SER cc_start: 0.8184 (m) cc_final: 0.7789 (p) REVERT: S 87 ARG cc_start: 0.7099 (mtt180) cc_final: 0.6704 (mtt90) REVERT: S 142 SER cc_start: 0.6865 (p) cc_final: 0.6352 (t) outliers start: 36 outliers final: 16 residues processed: 148 average time/residue: 1.2283 time to fit residues: 193.9104 Evaluate side-chains 142 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9307 Z= 0.168 Angle : 0.521 10.016 12613 Z= 0.271 Chirality : 0.040 0.132 1424 Planarity : 0.004 0.051 1588 Dihedral : 4.329 26.349 1260 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.02 % Favored : 97.89 % Rotamer: Outliers : 2.52 % Allowed : 16.53 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.15 (0.26), residues: 1139 helix: 1.84 (0.27), residues: 407 sheet: 0.56 (0.30), residues: 268 loop : 0.00 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.002 0.001 HIS G 44 PHE 0.024 0.001 PHE R 110 TYR 0.019 0.001 TYR R 93 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.018 Fit side-chains REVERT: R 36 MET cc_start: 0.5485 (tpp) cc_final: 0.3599 (tmm) REVERT: R 139 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.6729 (pmt-80) REVERT: R 162 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6332 (ptt) REVERT: R 241 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6488 (ptp-170) REVERT: R 272 MET cc_start: 0.6316 (mtm) cc_final: 0.6087 (ttp) REVERT: A 184 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7708 (tp) REVERT: A 198 MET cc_start: 0.7784 (ttm) cc_final: 0.7572 (ttp) REVERT: A 270 LYS cc_start: 0.7422 (mttt) cc_final: 0.7061 (mmpt) REVERT: A 274 PHE cc_start: 0.7167 (t80) cc_final: 0.6848 (t80) REVERT: B 57 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8357 (mttt) REVERT: B 217 MET cc_start: 0.8225 (pmm) cc_final: 0.7892 (pmt) REVERT: B 219 ARG cc_start: 0.7110 (mtt-85) cc_final: 0.6808 (mtm110) REVERT: B 254 ASP cc_start: 0.6638 (t70) cc_final: 0.6369 (t0) REVERT: B 322 ASP cc_start: 0.7877 (m-30) cc_final: 0.7642 (m-30) REVERT: S 6 GLU cc_start: 0.7769 (mp0) cc_final: 0.7295 (mp0) REVERT: S 23 SER cc_start: 0.8124 (t) cc_final: 0.7916 (m) REVERT: S 142 SER cc_start: 0.6900 (p) cc_final: 0.6559 (m) REVERT: S 174 GLN cc_start: 0.7970 (tt0) cc_final: 0.7632 (pt0) REVERT: S 222 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7726 (pt0) outliers start: 25 outliers final: 12 residues processed: 145 average time/residue: 1.2437 time to fit residues: 192.4338 Evaluate side-chains 137 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9307 Z= 0.358 Angle : 0.613 10.458 12613 Z= 0.320 Chirality : 0.045 0.188 1424 Planarity : 0.004 0.052 1588 Dihedral : 4.734 27.385 1260 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 3.73 % Allowed : 16.13 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.88 (0.25), residues: 1139 helix: 1.59 (0.26), residues: 407 sheet: 0.38 (0.30), residues: 273 loop : -0.10 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS G 44 PHE 0.028 0.002 PHE R 110 TYR 0.028 0.002 TYR R 93 ARG 0.003 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.117 Fit side-chains REVERT: R 36 MET cc_start: 0.5771 (tpp) cc_final: 0.3804 (tmm) REVERT: R 54 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5742 (m-10) REVERT: R 139 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.6654 (pmt-80) REVERT: R 162 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6229 (ptt) REVERT: R 241 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6695 (ptp-170) REVERT: R 272 MET cc_start: 0.6375 (mtm) cc_final: 0.6113 (ttp) REVERT: A 184 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7763 (tp) REVERT: A 198 MET cc_start: 0.7841 (ttm) cc_final: 0.7617 (ttp) REVERT: A 270 LYS cc_start: 0.7465 (mttt) cc_final: 0.7082 (mmpt) REVERT: A 274 PHE cc_start: 0.7283 (t80) cc_final: 0.6949 (t80) REVERT: B 57 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8506 (mttt) REVERT: B 217 MET cc_start: 0.8169 (pmm) cc_final: 0.7835 (pmt) REVERT: B 219 ARG cc_start: 0.7155 (mtt-85) cc_final: 0.6791 (mtm110) REVERT: B 254 ASP cc_start: 0.6702 (t70) cc_final: 0.6450 (t0) REVERT: B 322 ASP cc_start: 0.7909 (m-30) cc_final: 0.7682 (m-30) REVERT: S 23 SER cc_start: 0.8119 (t) cc_final: 0.7882 (m) REVERT: S 142 SER cc_start: 0.6916 (p) cc_final: 0.6703 (m) outliers start: 37 outliers final: 19 residues processed: 145 average time/residue: 1.1334 time to fit residues: 176.2271 Evaluate side-chains 141 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.0980 chunk 32 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 293 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9307 Z= 0.149 Angle : 0.523 11.828 12613 Z= 0.269 Chirality : 0.041 0.342 1424 Planarity : 0.004 0.052 1588 Dihedral : 4.235 25.955 1260 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.84 % Favored : 98.07 % Rotamer: Outliers : 2.32 % Allowed : 17.74 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.18 (0.26), residues: 1139 helix: 1.88 (0.26), residues: 413 sheet: 0.56 (0.30), residues: 271 loop : -0.01 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 297 HIS 0.003 0.001 HIS R 231 PHE 0.026 0.001 PHE R 286 TYR 0.022 0.001 TYR R 93 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.066 Fit side-chains REVERT: R 36 MET cc_start: 0.5607 (tpp) cc_final: 0.3702 (tmm) REVERT: R 139 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6638 (pmt-80) REVERT: R 162 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6194 (ptt) REVERT: R 272 MET cc_start: 0.6288 (mtm) cc_final: 0.6063 (ttp) REVERT: A 184 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7742 (tp) REVERT: A 198 MET cc_start: 0.7743 (ttm) cc_final: 0.7524 (ttp) REVERT: A 270 LYS cc_start: 0.7451 (mttt) cc_final: 0.7042 (mmpt) REVERT: A 274 PHE cc_start: 0.7126 (t80) cc_final: 0.6820 (t80) REVERT: B 217 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7797 (pmt) REVERT: B 219 ARG cc_start: 0.7131 (mtt-85) cc_final: 0.6774 (mtm110) REVERT: B 254 ASP cc_start: 0.6619 (t70) cc_final: 0.6352 (t0) REVERT: B 322 ASP cc_start: 0.7925 (m-30) cc_final: 0.7697 (m-30) REVERT: G 21 MET cc_start: 0.6463 (mmp) cc_final: 0.6227 (tpp) REVERT: S 6 GLU cc_start: 0.7763 (mp0) cc_final: 0.7505 (mt-10) REVERT: S 23 SER cc_start: 0.8119 (t) cc_final: 0.7902 (m) REVERT: S 142 SER cc_start: 0.6941 (p) cc_final: 0.6581 (m) REVERT: S 174 GLN cc_start: 0.7952 (tt0) cc_final: 0.7715 (pt0) REVERT: S 201 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7838 (t) REVERT: S 222 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7755 (pt0) outliers start: 23 outliers final: 9 residues processed: 140 average time/residue: 1.2445 time to fit residues: 186.8128 Evaluate side-chains 137 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9307 Z= 0.313 Angle : 0.585 11.667 12613 Z= 0.305 Chirality : 0.043 0.141 1424 Planarity : 0.004 0.053 1588 Dihedral : 4.587 27.090 1260 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.28 % Rotamer: Outliers : 2.02 % Allowed : 18.55 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.02 (0.26), residues: 1139 helix: 1.79 (0.26), residues: 410 sheet: 0.44 (0.30), residues: 272 loop : -0.11 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.031 0.002 PHE R 110 TYR 0.033 0.002 TYR R 93 ARG 0.003 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.092 Fit side-chains REVERT: R 36 MET cc_start: 0.5722 (tpp) cc_final: 0.3693 (tmm) REVERT: R 54 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5372 (m-10) REVERT: R 139 ARG cc_start: 0.7331 (mtm-85) cc_final: 0.6667 (pmt-80) REVERT: R 162 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6096 (ptt) REVERT: R 272 MET cc_start: 0.6343 (mtm) cc_final: 0.6107 (ttp) REVERT: A 184 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7770 (tp) REVERT: A 198 MET cc_start: 0.7832 (ttm) cc_final: 0.7576 (ttp) REVERT: A 270 LYS cc_start: 0.7455 (mttt) cc_final: 0.7066 (mmpt) REVERT: A 274 PHE cc_start: 0.7214 (t80) cc_final: 0.6916 (t80) REVERT: B 217 MET cc_start: 0.8149 (pmm) cc_final: 0.7823 (pmt) REVERT: B 219 ARG cc_start: 0.7156 (mtt-85) cc_final: 0.6791 (mtm110) REVERT: B 254 ASP cc_start: 0.6673 (t70) cc_final: 0.6426 (t0) REVERT: B 322 ASP cc_start: 0.7901 (m-30) cc_final: 0.7674 (m-30) REVERT: S 6 GLU cc_start: 0.7845 (mp0) cc_final: 0.7586 (mt-10) REVERT: S 23 SER cc_start: 0.8113 (t) cc_final: 0.7874 (m) REVERT: S 142 SER cc_start: 0.6786 (p) cc_final: 0.6447 (m) REVERT: S 174 GLN cc_start: 0.8016 (tt0) cc_final: 0.7651 (pt0) outliers start: 20 outliers final: 14 residues processed: 133 average time/residue: 1.1701 time to fit residues: 167.0646 Evaluate side-chains 136 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 103 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 293 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9307 Z= 0.268 Angle : 0.573 12.029 12613 Z= 0.296 Chirality : 0.043 0.267 1424 Planarity : 0.004 0.053 1588 Dihedral : 4.580 26.940 1260 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.11 % Favored : 97.72 % Rotamer: Outliers : 2.02 % Allowed : 19.05 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.99 (0.25), residues: 1139 helix: 1.79 (0.26), residues: 410 sheet: 0.39 (0.30), residues: 272 loop : -0.13 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.027 0.002 PHE R 110 TYR 0.034 0.002 TYR R 93 ARG 0.003 0.000 ARG R 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.286 Fit side-chains REVERT: R 36 MET cc_start: 0.5698 (tpp) cc_final: 0.3719 (tmm) REVERT: R 139 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.6643 (pmt-80) REVERT: R 272 MET cc_start: 0.6294 (mtm) cc_final: 0.6062 (ttp) REVERT: A 184 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7780 (tp) REVERT: A 198 MET cc_start: 0.7819 (ttm) cc_final: 0.7555 (ttp) REVERT: A 270 LYS cc_start: 0.7470 (mttt) cc_final: 0.7082 (mmpt) REVERT: A 274 PHE cc_start: 0.7204 (t80) cc_final: 0.6890 (t80) REVERT: B 217 MET cc_start: 0.8126 (pmm) cc_final: 0.7802 (pmt) REVERT: B 219 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.6789 (mtm110) REVERT: B 254 ASP cc_start: 0.6668 (t70) cc_final: 0.6406 (t0) REVERT: B 322 ASP cc_start: 0.7934 (m-30) cc_final: 0.7717 (m-30) REVERT: S 23 SER cc_start: 0.8110 (t) cc_final: 0.7884 (m) REVERT: S 142 SER cc_start: 0.6772 (p) cc_final: 0.6382 (m) REVERT: S 174 GLN cc_start: 0.8006 (tt0) cc_final: 0.7620 (pt0) outliers start: 20 outliers final: 14 residues processed: 130 average time/residue: 1.2161 time to fit residues: 169.6296 Evaluate side-chains 133 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.0570 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.119269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095749 restraints weight = 14473.542| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.66 r_work: 0.3206 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9307 Z= 0.189 Angle : 0.540 11.740 12613 Z= 0.278 Chirality : 0.041 0.140 1424 Planarity : 0.004 0.053 1588 Dihedral : 4.384 26.438 1260 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.28 % Favored : 97.54 % Rotamer: Outliers : 1.81 % Allowed : 19.35 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.11 (0.26), residues: 1139 helix: 1.94 (0.26), residues: 411 sheet: 0.41 (0.30), residues: 272 loop : -0.07 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS R 231 PHE 0.029 0.001 PHE R 110 TYR 0.039 0.002 TYR R 93 ARG 0.003 0.000 ARG R 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3812.61 seconds wall clock time: 67 minutes 26.97 seconds (4046.97 seconds total)