Starting phenix.real_space_refine on Fri Jul 19 16:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/07_2024/7xow_33361.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/07_2024/7xow_33361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/07_2024/7xow_33361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/07_2024/7xow_33361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/07_2024/7xow_33361.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/07_2024/7xow_33361.cif" } resolution = 3.1 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= 0.007 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 58 5.16 5 C 5479 2.51 5 N 1468 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 53": "OE1" <-> "OE2" Residue "R GLU 151": "OE1" <-> "OE2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R ARG 333": "NH1" <-> "NH2" Residue "R ARG 396": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" 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: 8566 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2153 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1716 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1798 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 75 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.21, per 1000 atoms: 0.61 Number of scatterers: 8566 At special positions: 0 Unit cell: (112.554, 115.596, 124.722, 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 58 16.00 O 1561 8.00 N 1468 7.00 C 5479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 36.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'R' and resid 54 through 81 Processing helix chain 'R' and resid 87 through 108 removed outlier: 4.032A pdb=" N ALA R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 118 Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 122 through 158 removed outlier: 4.142A pdb=" N ILE R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG R 158 " --> pdb=" O SER R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 166 removed outlier: 4.291A pdb=" N VAL R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 186 removed outlier: 3.711A pdb=" N ARG R 173 " --> pdb=" O SER R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 192 Processing helix chain 'R' and resid 214 through 228 Processing helix chain 'R' and resid 228 through 248 removed outlier: 3.832A pdb=" N GLY R 248 " --> pdb=" O GLU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 360 removed outlier: 4.413A pdb=" N VAL R 331 " --> pdb=" O ALA R 327 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 360 through 367 removed outlier: 3.876A pdb=" N HIS R 364 " --> pdb=" O GLY R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 370 through 391 removed outlier: 3.569A pdb=" N PHE R 374 " --> pdb=" O ALA R 370 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER R 382 " --> pdb=" O LEU R 378 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Proline residue: R 387 - end of helix Processing helix chain 'R' and resid 396 through 403 removed outlier: 3.787A pdb=" N ALA R 400 " --> pdb=" O ARG R 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.856A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.911A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.738A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.826A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.627A pdb=" N THR A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.036A pdb=" N TYR A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.710A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.813A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.888A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.704A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.583A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.534A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.737A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.916A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.557A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 134 through 136 Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AB3, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.689A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 183 through 189 removed outlier: 7.147A pdb=" N LEU A 34 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL A 198 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 36 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 200 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 38 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 35 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N MET A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 223 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 183 through 189 removed outlier: 7.147A pdb=" N LEU A 34 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL A 198 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 36 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 200 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 38 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 35 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N MET A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 223 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1188 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: 2.90 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1467 1.32 - 1.45: 2344 1.45 - 1.57: 4849 1.57 - 1.69: 1 1.69 - 1.82: 85 Bond restraints: 8746 Sorted by residual: bond pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" OH TYS L 12 " pdb=" S TYS L 12 " ideal model delta sigma weight residual 1.679 1.538 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C TYR R 189 " pdb=" O TYR R 189 " ideal model delta sigma weight residual 1.244 1.202 0.042 1.00e-02 1.00e+04 1.73e+01 bond pdb=" N LEU R 203 " pdb=" CA LEU R 203 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.64e+00 bond pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 1.458 1.482 -0.025 1.41e-02 5.03e+03 3.06e+00 ... (remaining 8741 not shown) Histogram of bond angle deviations from ideal: 84.47 - 94.38: 3 94.38 - 104.30: 118 104.30 - 114.21: 5168 114.21 - 124.13: 6381 124.13 - 134.05: 212 Bond angle restraints: 11882 Sorted by residual: angle pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " pdb=" O2 TYS L 12 " ideal model delta sigma weight residual 114.11 84.47 29.64 3.00e+00 1.11e-01 9.76e+01 angle pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " pdb=" O3 TYS L 12 " ideal model delta sigma weight residual 115.16 88.07 27.09 3.00e+00 1.11e-01 8.16e+01 angle pdb=" N VAL R 202 " pdb=" CA VAL R 202 " pdb=" C VAL R 202 " ideal model delta sigma weight residual 110.62 118.97 -8.35 1.02e+00 9.61e-01 6.71e+01 angle pdb=" N GLN R 204 " pdb=" CA GLN R 204 " pdb=" C GLN R 204 " ideal model delta sigma weight residual 111.17 121.67 -10.50 1.41e+00 5.03e-01 5.54e+01 angle pdb=" OH TYS L 12 " pdb=" S TYS L 12 " pdb=" O3 TYS L 12 " ideal model delta sigma weight residual 100.21 118.72 -18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 11877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4694 17.60 - 35.19: 391 35.19 - 52.79: 60 52.79 - 70.39: 10 70.39 - 87.98: 4 Dihedral angle restraints: 5159 sinusoidal: 1913 harmonic: 3246 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 137.28 42.72 0 5.00e+00 4.00e-02 7.30e+01 dihedral pdb=" C VAL R 202 " pdb=" N VAL R 202 " pdb=" CA VAL R 202 " pdb=" CB VAL R 202 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" CA LEU A 265 " pdb=" C LEU A 265 " pdb=" N PHE A 266 " pdb=" CA PHE A 266 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1186 0.067 - 0.134: 168 0.134 - 0.201: 10 0.201 - 0.269: 6 0.269 - 0.336: 4 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA PHE L 17 " pdb=" N PHE L 17 " pdb=" C PHE L 17 " pdb=" CB PHE L 17 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA GLN R 204 " pdb=" N GLN R 204 " pdb=" C GLN R 204 " pdb=" CB GLN R 204 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA VAL R 202 " pdb=" N VAL R 202 " pdb=" C VAL R 202 " pdb=" CB VAL R 202 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 1371 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 189 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO R 190 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO R 190 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 190 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO E 224 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 187 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO R 188 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO R 188 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 188 " -0.047 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 738 2.74 - 3.28: 8406 3.28 - 3.82: 13468 3.82 - 4.36: 16062 4.36 - 4.90: 29053 Nonbonded interactions: 67727 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.198 2.440 nonbonded pdb=" OD2 ASP B 228 " pdb=" NZ LYS A 209 " model vdw 2.244 2.520 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.250 2.520 nonbonded pdb=" OD1 ASP B 254 " pdb=" N ALA B 257 " model vdw 2.268 2.520 nonbonded pdb=" N CYS A 324 " pdb=" OD2 ASP A 327 " model vdw 2.269 2.520 ... (remaining 67722 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.280 Find NCS groups from input model: 0.090 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.005 0.170 8746 Z= 0.283 Angle : 0.857 29.645 11882 Z= 0.455 Chirality : 0.052 0.336 1374 Planarity : 0.006 0.105 1495 Dihedral : 13.161 87.985 3059 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -2.76 (0.23), residues: 1097 helix: -0.41 (0.26), residues: 364 sheet: -1.79 (0.29), residues: 289 loop : -3.05 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.003 0.001 HIS B 54 PHE 0.022 0.002 PHE B 234 TYR 0.013 0.001 TYR R 192 ARG 0.004 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 0.933 Fit side-chains REVERT: R 73 MET cc_start: 0.7231 (mmt) cc_final: 0.6878 (mmt) REVERT: R 207 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.5572 (m-70) REVERT: R 213 ARG cc_start: 0.6193 (mmt180) cc_final: 0.3788 (ptt-90) REVERT: R 333 ARG cc_start: 0.6314 (ttm170) cc_final: 0.5644 (ttm-80) REVERT: R 398 ARG cc_start: 0.7054 (mmt90) cc_final: 0.6744 (mmp80) REVERT: B 67 SER cc_start: 0.8803 (m) cc_final: 0.8404 (t) REVERT: B 325 MET cc_start: 0.7886 (tpp) cc_final: 0.7674 (tpp) REVERT: E 182 ASN cc_start: 0.8736 (m110) cc_final: 0.8462 (m110) REVERT: A 242 MET cc_start: 0.7403 (tpp) cc_final: 0.6316 (tpp) REVERT: A 305 LYS cc_start: 0.7059 (ttpp) cc_final: 0.6810 (tppt) REVERT: A 339 LYS cc_start: 0.7160 (tttt) cc_final: 0.6951 (tttp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2497 time to fit residues: 55.4276 Evaluate side-chains 136 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 0.0170 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 166 GLN R 196 GLN R 204 GLN B 17 GLN B 35 ASN B 75 GLN B 176 GLN B 220 GLN C 44 HIS E 159 ASN E 167 GLN E 171 GLN A 231 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8746 Z= 0.153 Angle : 0.568 8.392 11882 Z= 0.288 Chirality : 0.043 0.151 1374 Planarity : 0.005 0.081 1495 Dihedral : 4.639 38.397 1219 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 1.90 % Allowed : 10.19 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.50 (0.25), residues: 1097 helix: 0.97 (0.28), residues: 366 sheet: -1.33 (0.30), residues: 289 loop : -2.47 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE A 49 TYR 0.021 0.001 TYR R 380 ARG 0.003 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.865 Fit side-chains REVERT: R 207 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.5339 (m-70) REVERT: R 213 ARG cc_start: 0.6083 (mmt180) cc_final: 0.3731 (ptt-90) REVERT: R 333 ARG cc_start: 0.6317 (ttm170) cc_final: 0.5644 (ttm-80) REVERT: R 398 ARG cc_start: 0.6981 (mmt90) cc_final: 0.6775 (mmp80) REVERT: B 258 ASP cc_start: 0.8595 (t0) cc_final: 0.8010 (t0) REVERT: B 325 MET cc_start: 0.7939 (tpp) cc_final: 0.7459 (tpp) REVERT: E 70 ILE cc_start: 0.7639 (tt) cc_final: 0.7294 (tt) REVERT: A 242 MET cc_start: 0.7475 (tpp) cc_final: 0.6583 (tpp) REVERT: A 305 LYS cc_start: 0.6989 (ttpp) cc_final: 0.6751 (tppt) outliers start: 17 outliers final: 8 residues processed: 154 average time/residue: 0.1910 time to fit residues: 40.7968 Evaluate side-chains 137 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 40.0000 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN B 220 GLN A 321 HIS A 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8746 Z= 0.336 Angle : 0.667 8.967 11882 Z= 0.335 Chirality : 0.046 0.175 1374 Planarity : 0.005 0.092 1495 Dihedral : 5.013 43.012 1219 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 3.36 % Allowed : 12.88 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 1097 helix: 1.18 (0.28), residues: 366 sheet: -1.09 (0.30), residues: 298 loop : -2.40 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.002 PHE E 27 TYR 0.019 0.002 TYR A 285 ARG 0.003 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 0.976 Fit side-chains REVERT: R 207 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.5235 (m-70) REVERT: R 213 ARG cc_start: 0.6543 (mmt180) cc_final: 0.4117 (ptt-90) REVERT: R 333 ARG cc_start: 0.6521 (ttm170) cc_final: 0.5774 (ttm-80) REVERT: B 101 MET cc_start: 0.8492 (mtp) cc_final: 0.8269 (mtp) REVERT: B 118 ASP cc_start: 0.7766 (p0) cc_final: 0.7419 (p0) REVERT: B 137 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7504 (tpp-160) REVERT: B 164 THR cc_start: 0.9099 (p) cc_final: 0.8546 (m) REVERT: B 325 MET cc_start: 0.7991 (tpp) cc_final: 0.7597 (tpp) REVERT: E 126 ILE cc_start: 0.8091 (mp) cc_final: 0.7817 (mt) REVERT: E 146 SER cc_start: 0.8374 (t) cc_final: 0.8080 (p) REVERT: E 177 ILE cc_start: 0.8529 (pt) cc_final: 0.8300 (pt) REVERT: A 20 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: A 189 ASP cc_start: 0.7956 (t70) cc_final: 0.7755 (t0) REVERT: A 295 ASP cc_start: 0.5745 (OUTLIER) cc_final: 0.5191 (m-30) REVERT: A 306 MET cc_start: 0.6635 (mtm) cc_final: 0.6401 (mtp) REVERT: A 327 ASP cc_start: 0.6136 (OUTLIER) cc_final: 0.5824 (m-30) REVERT: L 15 MET cc_start: 0.6604 (ptp) cc_final: 0.6341 (mtp) outliers start: 30 outliers final: 21 residues processed: 147 average time/residue: 0.1994 time to fit residues: 40.6438 Evaluate side-chains 151 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN R 204 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN E 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8746 Z= 0.146 Angle : 0.555 8.086 11882 Z= 0.280 Chirality : 0.042 0.180 1374 Planarity : 0.004 0.076 1495 Dihedral : 4.573 37.533 1219 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.02 % Allowed : 14.22 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.76 (0.26), residues: 1097 helix: 1.57 (0.28), residues: 367 sheet: -0.91 (0.30), residues: 286 loop : -2.03 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 49 TYR 0.011 0.001 TYR E 178 ARG 0.003 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.002 Fit side-chains REVERT: R 184 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7386 (mp) REVERT: R 196 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.6396 (mp10) REVERT: R 204 GLN cc_start: 0.6414 (mt0) cc_final: 0.5623 (pt0) REVERT: R 333 ARG cc_start: 0.6230 (ttm170) cc_final: 0.5477 (ttm-80) REVERT: B 101 MET cc_start: 0.8441 (mtp) cc_final: 0.8223 (mtp) REVERT: B 137 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7522 (tpp-160) REVERT: B 258 ASP cc_start: 0.8394 (t0) cc_final: 0.8123 (t0) REVERT: B 325 MET cc_start: 0.7999 (tpp) cc_final: 0.7579 (tpp) REVERT: E 30 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.8099 (t) REVERT: E 116 THR cc_start: 0.6960 (OUTLIER) cc_final: 0.6653 (t) REVERT: E 126 ILE cc_start: 0.8112 (mp) cc_final: 0.7863 (mt) REVERT: E 146 SER cc_start: 0.8379 (t) cc_final: 0.8099 (p) REVERT: E 177 ILE cc_start: 0.8367 (pt) cc_final: 0.8101 (pt) REVERT: A 20 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: A 189 ASP cc_start: 0.7911 (t70) cc_final: 0.7691 (t0) REVERT: A 295 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5513 (m-30) REVERT: A 327 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: L 15 MET cc_start: 0.6683 (ptp) cc_final: 0.6299 (mtp) outliers start: 27 outliers final: 12 residues processed: 144 average time/residue: 0.2028 time to fit residues: 41.0514 Evaluate side-chains 134 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0670 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 0.0010 chunk 35 optimal weight: 0.3980 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN R 196 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8746 Z= 0.137 Angle : 0.546 7.646 11882 Z= 0.275 Chirality : 0.042 0.207 1374 Planarity : 0.004 0.074 1495 Dihedral : 4.284 34.937 1217 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.02 % Allowed : 15.90 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.48 (0.26), residues: 1097 helix: 1.90 (0.28), residues: 361 sheet: -0.78 (0.30), residues: 286 loop : -1.88 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 49 TYR 0.013 0.001 TYR A 285 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.952 Fit side-chains REVERT: R 90 ASN cc_start: 0.6630 (m110) cc_final: 0.5875 (m-40) REVERT: R 184 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7327 (mp) REVERT: R 196 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.6161 (mp10) REVERT: R 204 GLN cc_start: 0.6352 (mt0) cc_final: 0.5482 (pt0) REVERT: R 207 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.5255 (m-70) REVERT: R 333 ARG cc_start: 0.6141 (ttm170) cc_final: 0.5281 (ttm-80) REVERT: B 137 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7523 (tpp-160) REVERT: B 258 ASP cc_start: 0.8263 (t0) cc_final: 0.7880 (t0) REVERT: B 325 MET cc_start: 0.8011 (tpp) cc_final: 0.7588 (tpp) REVERT: E 146 SER cc_start: 0.8397 (t) cc_final: 0.8117 (p) REVERT: E 177 ILE cc_start: 0.8294 (pt) cc_final: 0.8021 (pt) REVERT: A 20 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: A 189 ASP cc_start: 0.7878 (t70) cc_final: 0.7656 (t0) REVERT: A 327 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6027 (m-30) REVERT: L 15 MET cc_start: 0.6619 (ptp) cc_final: 0.6192 (mtp) outliers start: 27 outliers final: 16 residues processed: 138 average time/residue: 0.1849 time to fit residues: 36.4076 Evaluate side-chains 139 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8746 Z= 0.290 Angle : 0.640 8.359 11882 Z= 0.322 Chirality : 0.045 0.229 1374 Planarity : 0.004 0.087 1495 Dihedral : 4.678 39.097 1217 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.70 % Allowed : 16.46 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1097 helix: 1.75 (0.28), residues: 361 sheet: -0.73 (0.30), residues: 297 loop : -1.97 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS R 364 PHE 0.017 0.002 PHE E 27 TYR 0.017 0.002 TYR A 285 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 0.968 Fit side-chains REVERT: R 184 LEU cc_start: 0.8094 (tt) cc_final: 0.7552 (mp) REVERT: R 204 GLN cc_start: 0.6421 (mt0) cc_final: 0.5567 (pt0) REVERT: R 213 ARG cc_start: 0.6505 (mmt180) cc_final: 0.3962 (ptt-90) REVERT: R 333 ARG cc_start: 0.6532 (ttm170) cc_final: 0.5806 (ttm-80) REVERT: B 118 ASP cc_start: 0.7794 (p0) cc_final: 0.7410 (p0) REVERT: B 137 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7504 (tpp-160) REVERT: B 325 MET cc_start: 0.8032 (tpp) cc_final: 0.7577 (tpp) REVERT: E 146 SER cc_start: 0.8350 (t) cc_final: 0.8113 (p) REVERT: E 177 ILE cc_start: 0.8389 (pt) cc_final: 0.8122 (pt) REVERT: A 20 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: A 189 ASP cc_start: 0.7911 (t70) cc_final: 0.7709 (t0) REVERT: A 270 LYS cc_start: 0.7355 (ttpt) cc_final: 0.7151 (ttmt) REVERT: A 327 ASP cc_start: 0.5929 (OUTLIER) cc_final: 0.5632 (m-30) REVERT: L 15 MET cc_start: 0.6773 (ptp) cc_final: 0.6155 (mtp) outliers start: 33 outliers final: 23 residues processed: 139 average time/residue: 0.2002 time to fit residues: 38.9965 Evaluate side-chains 142 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8746 Z= 0.228 Angle : 0.601 9.704 11882 Z= 0.301 Chirality : 0.043 0.243 1374 Planarity : 0.004 0.080 1495 Dihedral : 4.588 37.907 1217 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.80 % Allowed : 17.81 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.47 (0.26), residues: 1097 helix: 1.85 (0.28), residues: 360 sheet: -0.71 (0.31), residues: 287 loop : -1.86 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE E 27 TYR 0.014 0.001 TYR A 285 ARG 0.004 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.961 Fit side-chains REVERT: R 184 LEU cc_start: 0.7856 (tt) cc_final: 0.7279 (mp) REVERT: R 333 ARG cc_start: 0.6322 (ttm170) cc_final: 0.5554 (ttm-80) REVERT: B 118 ASP cc_start: 0.7675 (p0) cc_final: 0.7218 (p0) REVERT: B 137 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7507 (tpp-160) REVERT: B 205 ASP cc_start: 0.7554 (p0) cc_final: 0.7302 (t0) REVERT: B 325 MET cc_start: 0.8044 (tpp) cc_final: 0.7579 (tpp) REVERT: E 146 SER cc_start: 0.8337 (t) cc_final: 0.8105 (p) REVERT: E 177 ILE cc_start: 0.8359 (pt) cc_final: 0.8092 (pt) REVERT: E 180 MET cc_start: 0.7867 (ptm) cc_final: 0.7665 (ptm) REVERT: A 20 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: A 189 ASP cc_start: 0.7912 (t70) cc_final: 0.7702 (t0) REVERT: A 327 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5908 (m-30) REVERT: L 15 MET cc_start: 0.6604 (ptp) cc_final: 0.6272 (mtp) outliers start: 25 outliers final: 19 residues processed: 133 average time/residue: 0.1846 time to fit residues: 35.4293 Evaluate side-chains 138 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN R 204 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8746 Z= 0.221 Angle : 0.617 12.325 11882 Z= 0.304 Chirality : 0.044 0.307 1374 Planarity : 0.004 0.079 1495 Dihedral : 4.574 37.113 1217 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.91 % Allowed : 18.03 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.42 (0.26), residues: 1097 helix: 1.93 (0.28), residues: 360 sheet: -0.72 (0.31), residues: 287 loop : -1.84 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE E 27 TYR 0.015 0.001 TYR A 285 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.898 Fit side-chains REVERT: R 184 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7299 (mp) REVERT: R 333 ARG cc_start: 0.6331 (ttm170) cc_final: 0.5558 (ttm-80) REVERT: B 118 ASP cc_start: 0.7657 (p0) cc_final: 0.7203 (p0) REVERT: B 137 ARG cc_start: 0.7869 (mmm160) cc_final: 0.7488 (tpp-160) REVERT: B 325 MET cc_start: 0.8047 (tpp) cc_final: 0.7648 (tpp) REVERT: E 146 SER cc_start: 0.8372 (t) cc_final: 0.8141 (p) REVERT: E 177 ILE cc_start: 0.8367 (pt) cc_final: 0.8097 (pt) REVERT: A 20 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: A 189 ASP cc_start: 0.7914 (t70) cc_final: 0.7703 (t0) REVERT: A 327 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6296 (m-30) REVERT: L 15 MET cc_start: 0.6768 (ptp) cc_final: 0.6392 (mtp) outliers start: 26 outliers final: 19 residues processed: 129 average time/residue: 0.1858 time to fit residues: 34.2776 Evaluate side-chains 136 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN R 204 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8746 Z= 0.165 Angle : 0.590 9.440 11882 Z= 0.301 Chirality : 0.043 0.273 1374 Planarity : 0.004 0.074 1495 Dihedral : 4.384 34.120 1217 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.80 % Allowed : 18.14 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.26 (0.26), residues: 1097 helix: 2.03 (0.28), residues: 363 sheet: -0.62 (0.31), residues: 284 loop : -1.75 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 321 PHE 0.015 0.001 PHE A 49 TYR 0.015 0.001 TYR A 285 ARG 0.002 0.000 ARG R 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: R 184 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7526 (mp) REVERT: R 333 ARG cc_start: 0.6202 (ttm170) cc_final: 0.5347 (ttm-80) REVERT: R 402 LEU cc_start: 0.5673 (tt) cc_final: 0.4913 (mp) REVERT: B 137 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7484 (tpp-160) REVERT: B 325 MET cc_start: 0.8026 (tpp) cc_final: 0.7626 (tpp) REVERT: E 146 SER cc_start: 0.8374 (t) cc_final: 0.8147 (p) REVERT: E 177 ILE cc_start: 0.8300 (pt) cc_final: 0.8030 (pt) REVERT: E 180 MET cc_start: 0.7591 (ptm) cc_final: 0.7391 (ptm) REVERT: A 20 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: A 189 ASP cc_start: 0.7896 (t70) cc_final: 0.7669 (t0) REVERT: A 227 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.8042 (t) REVERT: A 327 ASP cc_start: 0.6600 (OUTLIER) cc_final: 0.6271 (m-30) REVERT: L 15 MET cc_start: 0.6735 (ptp) cc_final: 0.5940 (mtp) outliers start: 25 outliers final: 20 residues processed: 133 average time/residue: 0.2125 time to fit residues: 40.0527 Evaluate side-chains 138 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8746 Z= 0.163 Angle : 0.592 9.643 11882 Z= 0.298 Chirality : 0.042 0.231 1374 Planarity : 0.004 0.073 1495 Dihedral : 4.323 33.262 1217 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.69 % Allowed : 18.37 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 (0.26), residues: 1097 helix: 2.13 (0.28), residues: 363 sheet: -0.65 (0.30), residues: 289 loop : -1.65 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS C 44 PHE 0.015 0.001 PHE A 49 TYR 0.014 0.001 TYR A 285 ARG 0.005 0.000 ARG R 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: R 134 MET cc_start: 0.7056 (mmm) cc_final: 0.6815 (mtp) REVERT: R 184 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7554 (mp) REVERT: R 333 ARG cc_start: 0.6195 (ttm170) cc_final: 0.5337 (ttm-80) REVERT: B 22 ARG cc_start: 0.6585 (ttm170) cc_final: 0.6369 (ttm170) REVERT: B 118 ASP cc_start: 0.7278 (p0) cc_final: 0.6797 (p0) REVERT: B 137 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7489 (tpp-160) REVERT: B 325 MET cc_start: 0.8028 (tpp) cc_final: 0.7623 (tpp) REVERT: E 146 SER cc_start: 0.8383 (t) cc_final: 0.8157 (p) REVERT: E 177 ILE cc_start: 0.8293 (pt) cc_final: 0.8013 (pt) REVERT: E 180 MET cc_start: 0.7543 (ptm) cc_final: 0.7312 (ptm) REVERT: A 20 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: A 189 ASP cc_start: 0.7897 (t70) cc_final: 0.7674 (t0) REVERT: A 227 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.8059 (t) REVERT: A 327 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6211 (m-30) REVERT: L 15 MET cc_start: 0.6868 (ptp) cc_final: 0.6052 (mtp) outliers start: 24 outliers final: 19 residues processed: 127 average time/residue: 0.1879 time to fit residues: 34.1080 Evaluate side-chains 134 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139402 restraints weight = 9244.917| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.96 r_work: 0.3654 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8746 Z= 0.163 Angle : 0.587 9.611 11882 Z= 0.293 Chirality : 0.042 0.236 1374 Planarity : 0.004 0.072 1495 Dihedral : 4.301 33.586 1217 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.02 % Allowed : 18.03 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.08 (0.26), residues: 1097 helix: 2.17 (0.28), residues: 363 sheet: -0.59 (0.30), residues: 288 loop : -1.59 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.005 0.001 HIS C 44 PHE 0.016 0.001 PHE A 49 TYR 0.013 0.001 TYR A 285 ARG 0.002 0.000 ARG R 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.77 seconds wall clock time: 36 minutes 14.11 seconds (2174.11 seconds total)