Starting phenix.real_space_refine on Fri Mar 15 07:01:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/03_2024/7ra3_24334_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/03_2024/7ra3_24334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/03_2024/7ra3_24334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/03_2024/7ra3_24334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/03_2024/7ra3_24334_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/03_2024/7ra3_24334_neut.pdb" } resolution = 3.24 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= 0.001 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 64 5.16 5 C 6859 2.51 5 N 1894 2.21 5 O 1985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 3": "OE1" <-> "OE2" Residue "P PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 136": "NH1" <-> "NH2" Residue "R TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 169": "NH1" <-> "NH2" Residue "R PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 192": "NH1" <-> "NH2" Residue "R ARG 257": "NH1" <-> "NH2" Residue "R TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 291": "OE1" <-> "OE2" Residue "R ARG 300": "NH1" <-> "NH2" Residue "R ARG 328": "NH1" <-> "NH2" Residue "R TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "R ARG 341": "NH1" <-> "NH2" Residue "R ARG 405": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10802 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1792 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1747 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 262 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3001 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA R 53 " occ=0.70 ... (3 atoms not shown) pdb=" CB ALA R 53 " occ=0.70 Time building chain proxies: 6.24, per 1000 atoms: 0.58 Number of scatterers: 10802 At special positions: 0 Unit cell: (167.184, 123.12, 104.976, 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 64 16.00 O 1985 8.00 N 1894 7.00 C 6859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 70 " distance=2.02 Simple disulfide: pdb=" SG CYS R 61 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 84 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " 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: 4.36 Conformation dependent library (CDL) restraints added in 2.0 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2570 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 16 sheets defined 36.6% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 removed outlier: 3.541A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.778A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.677A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.820A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.158A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.832A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.861A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.797A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.840A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.591A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.817A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.619A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'P' and resid 30 through 32 No H-bonds generated for 'chain 'P' and resid 30 through 32' Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.782A pdb=" N GLN R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 93 removed outlier: 4.083A pdb=" N HIS R 92 " --> pdb=" O PRO R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 162 removed outlier: 4.321A pdb=" N PHE R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 194 Processing helix chain 'R' and resid 208 through 246 Processing helix chain 'R' and resid 253 through 281 removed outlier: 3.634A pdb=" N LEU R 261 " --> pdb=" O ARG R 257 " (cutoff:3.500A) Proline residue: R 267 - end of helix removed outlier: 3.787A pdb=" N ILE R 272 " --> pdb=" O ALA R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 328 removed outlier: 3.609A pdb=" N TRP R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 336 through 351 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 356 Processing helix chain 'R' and resid 362 through 367 Processing helix chain 'R' and resid 370 through 393 removed outlier: 3.758A pdb=" N PHE R 376 " --> pdb=" O ALA R 372 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU R 377 " --> pdb=" O LYS R 373 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 410 removed outlier: 3.743A pdb=" N HIS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.589A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 360 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.871A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.929A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.855A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 149 removed outlier: 4.430A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.102A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.720A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.566A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.094A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.565A pdb=" N ARG E 148 " --> pdb=" O THR E 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 135 removed outlier: 3.672A pdb=" N VAL E 135 " --> pdb=" O LYS E 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.654A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.604A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 78 through 80 518 hydrogen bonds defined for protein. 1431 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: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2019 1.33 - 1.45: 2954 1.45 - 1.57: 5977 1.57 - 1.70: 1 1.70 - 1.82: 89 Bond restraints: 11040 Sorted by residual: bond pdb=" C THR B 243 " pdb=" N GLY B 244 " ideal model delta sigma weight residual 1.331 1.312 0.019 6.60e-03 2.30e+04 8.56e+00 bond pdb=" N ASP B 247 " pdb=" CA ASP B 247 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.12e+00 bond pdb=" C PRO G 49 " pdb=" O PRO G 49 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.30e-02 5.92e+03 5.92e+00 bond pdb=" C THR B 243 " pdb=" O THR B 243 " ideal model delta sigma weight residual 1.235 1.207 0.027 1.13e-02 7.83e+03 5.86e+00 bond pdb=" N ASP G 48 " pdb=" CA ASP G 48 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.25e-02 6.40e+03 4.35e+00 ... (remaining 11035 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.28: 233 106.28 - 113.23: 5804 113.23 - 120.17: 4122 120.17 - 127.12: 4662 127.12 - 134.07: 154 Bond angle restraints: 14975 Sorted by residual: angle pdb=" C ASP G 48 " pdb=" CA ASP G 48 " pdb=" CB ASP G 48 " ideal model delta sigma weight residual 110.17 103.94 6.23 1.11e+00 8.12e-01 3.15e+01 angle pdb=" N GLN R 285 " pdb=" CA GLN R 285 " pdb=" C GLN R 285 " ideal model delta sigma weight residual 110.80 99.33 11.47 2.13e+00 2.20e-01 2.90e+01 angle pdb=" CA ARG G 13 " pdb=" CB ARG G 13 " pdb=" CG ARG G 13 " ideal model delta sigma weight residual 114.10 122.96 -8.86 2.00e+00 2.50e-01 1.96e+01 angle pdb=" CB GLN R 285 " pdb=" CG GLN R 285 " pdb=" CD GLN R 285 " ideal model delta sigma weight residual 112.60 119.85 -7.25 1.70e+00 3.46e-01 1.82e+01 angle pdb=" CA GLU A 230 " pdb=" C GLU A 230 " pdb=" O GLU A 230 " ideal model delta sigma weight residual 121.58 116.92 4.66 1.12e+00 7.97e-01 1.73e+01 ... (remaining 14970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 5804 16.54 - 33.08: 583 33.08 - 49.62: 104 49.62 - 66.16: 13 66.16 - 82.70: 11 Dihedral angle restraints: 6515 sinusoidal: 2523 harmonic: 3992 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 143.26 -50.26 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CA ARG N 38 " pdb=" C ARG N 38 " pdb=" N GLN N 39 " pdb=" CA GLN N 39 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LYS A 211 " pdb=" C LYS A 211 " pdb=" N PHE A 212 " pdb=" CA PHE A 212 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1194 0.045 - 0.091: 348 0.091 - 0.136: 107 0.136 - 0.181: 15 0.181 - 0.226: 3 Chirality restraints: 1667 Sorted by residual: chirality pdb=" CG LEU A 388 " pdb=" CB LEU A 388 " pdb=" CD1 LEU A 388 " pdb=" CD2 LEU A 388 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU B 261 " pdb=" CB LEU B 261 " pdb=" CD1 LEU B 261 " pdb=" CD2 LEU B 261 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 1664 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " 0.013 2.00e-02 2.50e+03 2.23e-02 1.24e+01 pdb=" CG TRP E 111 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.025 2.00e-02 2.50e+03 2.23e-02 9.96e+00 pdb=" CG TYR B 59 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 75 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO R 76 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 76 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 76 " -0.042 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 181 2.64 - 3.20: 10500 3.20 - 3.77: 17195 3.77 - 4.33: 23312 4.33 - 4.90: 38344 Nonbonded interactions: 89532 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.074 2.440 nonbonded pdb=" ND2 ASN R 310 " pdb=" O LEU R 350 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.228 2.440 nonbonded pdb=" O PRO A 332 " pdb=" OG1 THR A 335 " model vdw 2.241 2.440 nonbonded pdb=" O GLN E 113 " pdb=" OG SER E 172 " model vdw 2.260 2.440 ... (remaining 89527 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=0.50 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: 3.110 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: 13.810 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.460 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 0.086 11040 Z= 0.349 Angle : 0.905 11.467 14975 Z= 0.481 Chirality : 0.048 0.226 1667 Planarity : 0.005 0.075 1909 Dihedral : 13.678 82.697 3921 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.35 % Allowed : 0.35 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.87 (0.23), residues: 1349 helix: -0.50 (0.23), residues: 446 sheet: -1.67 (0.26), residues: 350 loop : -1.39 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 111 HIS 0.019 0.002 HIS A 357 PHE 0.033 0.002 PHE P 6 TYR 0.055 0.002 TYR B 59 ARG 0.033 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 24 ASN cc_start: 0.8967 (m110) cc_final: 0.8643 (m-40) REVERT: R 237 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8084 (tm-30) outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.2646 time to fit residues: 77.1647 Evaluate side-chains 163 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.2980 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.0010 chunk 122 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 171 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN R 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11040 Z= 0.194 Angle : 0.676 13.070 14975 Z= 0.342 Chirality : 0.044 0.178 1667 Planarity : 0.004 0.057 1909 Dihedral : 5.215 32.274 1515 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.76 % Allowed : 12.05 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.41 (0.23), residues: 1349 helix: 0.02 (0.24), residues: 439 sheet: -1.35 (0.27), residues: 338 loop : -1.30 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 111 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.024 0.002 TYR R 259 ARG 0.007 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 18 LEU cc_start: 0.7182 (mt) cc_final: 0.6835 (mt) REVERT: N 29 PHE cc_start: 0.8647 (t80) cc_final: 0.8397 (t80) REVERT: N 69 THR cc_start: 0.8392 (m) cc_final: 0.8148 (t) REVERT: P 24 ASN cc_start: 0.8959 (m110) cc_final: 0.8602 (m-40) REVERT: R 237 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7989 (tm-30) outliers start: 20 outliers final: 13 residues processed: 204 average time/residue: 0.2408 time to fit residues: 68.8410 Evaluate side-chains 177 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11040 Z= 0.323 Angle : 0.693 10.715 14975 Z= 0.357 Chirality : 0.045 0.217 1667 Planarity : 0.005 0.055 1909 Dihedral : 5.117 34.951 1514 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.31 % Allowed : 15.04 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.39 (0.23), residues: 1349 helix: 0.11 (0.24), residues: 444 sheet: -1.35 (0.27), residues: 344 loop : -1.35 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 233 HIS 0.006 0.001 HIS B 266 PHE 0.022 0.002 PHE P 6 TYR 0.025 0.002 TYR R 259 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8529 (pp) REVERT: B 210 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8343 (tp) REVERT: N 69 THR cc_start: 0.8463 (m) cc_final: 0.8150 (t) REVERT: P 14 MET cc_start: 0.8085 (mmm) cc_final: 0.7845 (mmm) REVERT: P 24 ASN cc_start: 0.8994 (m110) cc_final: 0.8638 (m-40) REVERT: R 165 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6570 (pp) REVERT: R 237 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8032 (tm-30) outliers start: 49 outliers final: 28 residues processed: 208 average time/residue: 0.2082 time to fit residues: 62.8410 Evaluate side-chains 193 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 242 HIS R 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11040 Z= 0.250 Angle : 0.658 9.678 14975 Z= 0.335 Chirality : 0.043 0.201 1667 Planarity : 0.004 0.055 1909 Dihedral : 4.935 35.733 1514 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.13 % Allowed : 16.89 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.22 (0.23), residues: 1349 helix: 0.30 (0.25), residues: 444 sheet: -1.22 (0.27), residues: 339 loop : -1.33 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 297 HIS 0.006 0.001 HIS B 266 PHE 0.017 0.001 PHE P 6 TYR 0.021 0.002 TYR R 259 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 182 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8463 (pp) REVERT: B 210 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8261 (tp) REVERT: E 232 LYS cc_start: 0.8236 (pptt) cc_final: 0.8027 (pptt) REVERT: G 11 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8643 (tm-30) REVERT: N 69 THR cc_start: 0.8425 (m) cc_final: 0.8216 (p) REVERT: N 123 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7764 (tm-30) REVERT: P 14 MET cc_start: 0.8127 (mmm) cc_final: 0.7861 (mmm) REVERT: P 18 HIS cc_start: 0.7837 (m-70) cc_final: 0.7614 (m170) REVERT: P 24 ASN cc_start: 0.9001 (m110) cc_final: 0.8648 (m110) REVERT: R 165 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6529 (pp) REVERT: R 237 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8075 (tm-30) outliers start: 47 outliers final: 33 residues processed: 213 average time/residue: 0.2096 time to fit residues: 64.3528 Evaluate side-chains 204 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 6.9990 chunk 74 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11040 Z= 0.166 Angle : 0.630 7.897 14975 Z= 0.315 Chirality : 0.042 0.222 1667 Planarity : 0.004 0.052 1909 Dihedral : 4.608 33.055 1514 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.31 % Allowed : 18.21 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.97 (0.24), residues: 1349 helix: 0.59 (0.25), residues: 437 sheet: -1.17 (0.27), residues: 351 loop : -1.17 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 297 HIS 0.005 0.001 HIS B 266 PHE 0.015 0.001 PHE A 212 TYR 0.020 0.001 TYR R 259 ARG 0.005 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7693 (p0) cc_final: 0.7081 (p0) REVERT: B 210 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8152 (tp) REVERT: N 69 THR cc_start: 0.8427 (m) cc_final: 0.8227 (p) REVERT: N 123 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7768 (tm-30) REVERT: P 14 MET cc_start: 0.8192 (mmm) cc_final: 0.7855 (mmm) REVERT: P 15 ASP cc_start: 0.8717 (t70) cc_final: 0.8225 (t70) REVERT: P 24 ASN cc_start: 0.9016 (m110) cc_final: 0.8658 (m-40) REVERT: R 159 LEU cc_start: 0.8294 (tp) cc_final: 0.7933 (mp) REVERT: R 165 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6685 (pp) outliers start: 49 outliers final: 30 residues processed: 228 average time/residue: 0.2126 time to fit residues: 69.6534 Evaluate side-chains 206 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 334 ASP Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11040 Z= 0.190 Angle : 0.646 8.791 14975 Z= 0.323 Chirality : 0.042 0.173 1667 Planarity : 0.004 0.050 1909 Dihedral : 4.537 32.982 1514 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.22 % Allowed : 19.44 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.91 (0.24), residues: 1349 helix: 0.68 (0.25), residues: 437 sheet: -1.08 (0.28), residues: 343 loop : -1.22 (0.28), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 297 HIS 0.006 0.001 HIS B 266 PHE 0.017 0.001 PHE N 68 TYR 0.021 0.001 TYR R 259 ARG 0.002 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 188 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8521 (mtpp) REVERT: B 210 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8148 (tp) REVERT: N 69 THR cc_start: 0.8397 (m) cc_final: 0.8161 (p) REVERT: P 14 MET cc_start: 0.8101 (mmm) cc_final: 0.7876 (mmm) REVERT: P 15 ASP cc_start: 0.8718 (t70) cc_final: 0.8228 (t70) REVERT: P 24 ASN cc_start: 0.9041 (m110) cc_final: 0.8688 (m-40) REVERT: R 159 LEU cc_start: 0.8315 (tp) cc_final: 0.7962 (mp) REVERT: R 165 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6633 (pp) outliers start: 48 outliers final: 35 residues processed: 218 average time/residue: 0.2255 time to fit residues: 70.5202 Evaluate side-chains 208 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 334 ASP Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 0.0060 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11040 Z= 0.160 Angle : 0.642 9.516 14975 Z= 0.317 Chirality : 0.042 0.179 1667 Planarity : 0.004 0.053 1909 Dihedral : 4.346 31.768 1514 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.22 % Allowed : 19.70 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.85 (0.24), residues: 1349 helix: 0.80 (0.25), residues: 435 sheet: -1.08 (0.28), residues: 340 loop : -1.22 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.005 0.001 HIS B 266 PHE 0.022 0.001 PHE P 6 TYR 0.019 0.001 TYR R 259 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 194 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8215 (tp) REVERT: E 161 TYR cc_start: 0.8304 (m-80) cc_final: 0.8102 (m-80) REVERT: N 69 THR cc_start: 0.8397 (m) cc_final: 0.8143 (p) REVERT: P 14 MET cc_start: 0.8141 (mmm) cc_final: 0.7922 (mmm) REVERT: P 15 ASP cc_start: 0.8600 (t70) cc_final: 0.8219 (t70) REVERT: P 24 ASN cc_start: 0.9055 (m110) cc_final: 0.8693 (m-40) REVERT: R 165 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6588 (pp) REVERT: R 259 TYR cc_start: 0.7885 (p90) cc_final: 0.7574 (p90) outliers start: 48 outliers final: 33 residues processed: 225 average time/residue: 0.2105 time to fit residues: 68.4908 Evaluate side-chains 209 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.0020 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11040 Z= 0.165 Angle : 0.641 10.172 14975 Z= 0.316 Chirality : 0.042 0.168 1667 Planarity : 0.004 0.048 1909 Dihedral : 4.267 28.256 1514 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.52 % Allowed : 20.49 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1349 helix: 0.91 (0.26), residues: 437 sheet: -1.06 (0.28), residues: 339 loop : -1.11 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.006 0.001 HIS B 266 PHE 0.020 0.001 PHE P 6 TYR 0.020 0.001 TYR R 259 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 93 MET cc_start: 0.7616 (tpt) cc_final: 0.7355 (tpt) REVERT: N 29 PHE cc_start: 0.8756 (t80) cc_final: 0.8436 (t80) REVERT: N 69 THR cc_start: 0.8372 (m) cc_final: 0.8147 (p) REVERT: P 15 ASP cc_start: 0.8570 (t70) cc_final: 0.8188 (t70) REVERT: P 24 ASN cc_start: 0.9044 (m110) cc_final: 0.8658 (m110) REVERT: R 165 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6493 (pp) REVERT: R 181 MET cc_start: 0.8007 (ttp) cc_final: 0.7762 (ttm) outliers start: 40 outliers final: 31 residues processed: 214 average time/residue: 0.2133 time to fit residues: 66.0179 Evaluate side-chains 214 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 334 ASP Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.0040 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.0000 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11040 Z= 0.161 Angle : 0.660 10.760 14975 Z= 0.324 Chirality : 0.042 0.205 1667 Planarity : 0.004 0.048 1909 Dihedral : 4.199 26.614 1514 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.64 % Allowed : 21.81 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.61 (0.24), residues: 1349 helix: 1.00 (0.26), residues: 437 sheet: -0.99 (0.28), residues: 327 loop : -1.06 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 339 HIS 0.006 0.001 HIS B 266 PHE 0.020 0.001 PHE A 222 TYR 0.020 0.001 TYR R 259 ARG 0.005 0.000 ARG R 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 93 MET cc_start: 0.7670 (tpt) cc_final: 0.7453 (tpt) REVERT: N 29 PHE cc_start: 0.8734 (t80) cc_final: 0.8442 (t80) REVERT: N 69 THR cc_start: 0.8358 (m) cc_final: 0.8125 (p) REVERT: P 15 ASP cc_start: 0.8463 (t70) cc_final: 0.8073 (t70) REVERT: P 24 ASN cc_start: 0.9054 (m110) cc_final: 0.8716 (m-40) REVERT: R 181 MET cc_start: 0.7969 (ttp) cc_final: 0.7751 (ttm) outliers start: 30 outliers final: 28 residues processed: 211 average time/residue: 0.2256 time to fit residues: 67.2776 Evaluate side-chains 204 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 334 ASP Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.0020 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 0.7508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11040 Z= 0.177 Angle : 0.684 10.813 14975 Z= 0.336 Chirality : 0.042 0.236 1667 Planarity : 0.004 0.047 1909 Dihedral : 4.202 25.710 1514 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.25 % Allowed : 21.81 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.61 (0.24), residues: 1349 helix: 0.96 (0.26), residues: 443 sheet: -0.93 (0.28), residues: 346 loop : -1.07 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 297 HIS 0.010 0.001 HIS A 220 PHE 0.020 0.001 PHE N 68 TYR 0.020 0.001 TYR R 259 ARG 0.003 0.000 ARG R 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 93 MET cc_start: 0.7687 (tpt) cc_final: 0.7459 (tpt) REVERT: N 29 PHE cc_start: 0.8731 (t80) cc_final: 0.8436 (t80) REVERT: N 68 PHE cc_start: 0.8166 (m-80) cc_final: 0.7520 (m-80) REVERT: N 69 THR cc_start: 0.8412 (m) cc_final: 0.8134 (p) REVERT: P 15 ASP cc_start: 0.8482 (t70) cc_final: 0.8102 (t70) REVERT: P 24 ASN cc_start: 0.9013 (m110) cc_final: 0.8680 (m110) REVERT: R 165 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6459 (pp) REVERT: R 181 MET cc_start: 0.7990 (ttp) cc_final: 0.7763 (ttm) outliers start: 37 outliers final: 31 residues processed: 211 average time/residue: 0.2204 time to fit residues: 66.7855 Evaluate side-chains 214 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 334 ASP Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 0.0050 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 HIS ** 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 = 0.3894 r_free = 0.3894 target = 0.098473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078666 restraints weight = 33549.582| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.09 r_work: 0.3398 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11040 Z= 0.169 Angle : 0.682 10.836 14975 Z= 0.334 Chirality : 0.042 0.215 1667 Planarity : 0.004 0.048 1909 Dihedral : 4.217 28.152 1514 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.99 % Allowed : 22.08 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.58 (0.24), residues: 1349 helix: 1.00 (0.26), residues: 443 sheet: -0.88 (0.28), residues: 341 loop : -1.11 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 297 HIS 0.009 0.001 HIS B 266 PHE 0.033 0.001 PHE N 68 TYR 0.020 0.001 TYR R 259 ARG 0.005 0.000 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.57 seconds wall clock time: 49 minutes 26.65 seconds (2966.65 seconds total)