Starting phenix.real_space_refine (version: dev) on Sun Feb 19 23:55:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/02_2023/7ra3_24334_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/02_2023/7ra3_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_24334/02_2023/7ra3_24334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/02_2023/7ra3_24334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/02_2023/7ra3_24334_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra3_24334/02_2023/7ra3_24334_neut.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 6.02, per 1000 atoms: 0.56 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: 4.09 Conformation dependent library (CDL) restraints added in 1.4 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: 0.55 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: 3.37 Time building geometry restraints manager: 4.41 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 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. 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 14.190 Check model and map are aligned: 0.170 Process input model: 29.190 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 % 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 *********************** 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 : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.2697 time to fit residues: 79.0311 Evaluate side-chains 162 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0942 time to fit residues: 1.8338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 24 ASN ** 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: 0.7999 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11040 Z= 0.196 Angle : 0.677 11.374 14975 Z= 0.343 Chirality : 0.044 0.165 1667 Planarity : 0.004 0.057 1909 Dihedral : 5.176 32.435 1514 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.58 % 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: -1.42 (0.23), residues: 1349 helix: 0.01 (0.24), residues: 439 sheet: -1.35 (0.27), residues: 338 loop : -1.31 (0.28), residues: 572 *********************** 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 209 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 202 average time/residue: 0.2470 time to fit residues: 69.7370 Evaluate side-chains 176 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1418 time to fit residues: 4.9265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 102 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.9764 ------------------------------------------------------------------------------- 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** ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS R 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11040 Z= 0.255 Angle : 0.664 10.400 14975 Z= 0.340 Chirality : 0.044 0.225 1667 Planarity : 0.004 0.053 1909 Dihedral : 4.982 36.599 1514 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 2.90 % 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: -1.29 (0.23), residues: 1349 helix: 0.19 (0.24), residues: 440 sheet: -1.31 (0.27), residues: 344 loop : -1.28 (0.28), residues: 565 *********************** 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 215 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 206 average time/residue: 0.2173 time to fit residues: 65.3334 Evaluate side-chains 178 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1045 time to fit residues: 4.2899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 130 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- 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** ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 HIS R 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 11040 Z= 0.326 Angle : 0.693 9.437 14975 Z= 0.355 Chirality : 0.045 0.198 1667 Planarity : 0.004 0.055 1909 Dihedral : 5.051 35.879 1514 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 2.55 % 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: -1.23 (0.23), residues: 1349 helix: 0.33 (0.25), residues: 440 sheet: -1.24 (0.27), residues: 344 loop : -1.36 (0.28), residues: 565 *********************** 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 203 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 194 average time/residue: 0.2278 time to fit residues: 64.0172 Evaluate side-chains 172 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1079 time to fit residues: 4.9508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11040 Z= 0.220 Angle : 0.650 7.993 14975 Z= 0.328 Chirality : 0.043 0.214 1667 Planarity : 0.004 0.053 1909 Dihedral : 4.774 32.942 1514 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 2.46 % 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: -1.07 (0.23), residues: 1349 helix: 0.45 (0.25), residues: 440 sheet: -1.16 (0.27), residues: 348 loop : -1.24 (0.28), residues: 561 *********************** 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 218 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 206 average time/residue: 0.2100 time to fit residues: 63.5972 Evaluate side-chains 180 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1291 time to fit residues: 3.9444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 125 optimal weight: 0.1980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11040 Z= 0.227 Angle : 0.675 8.832 14975 Z= 0.338 Chirality : 0.043 0.236 1667 Planarity : 0.004 0.051 1909 Dihedral : 4.737 34.058 1514 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 2.55 % 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: -1.04 (0.24), residues: 1349 helix: 0.49 (0.25), residues: 443 sheet: -1.14 (0.27), residues: 350 loop : -1.23 (0.28), residues: 556 *********************** 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 211 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.357 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 198 average time/residue: 0.2353 time to fit residues: 66.6890 Evaluate side-chains 181 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1059 time to fit residues: 4.6833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11040 Z= 0.203 Angle : 0.673 8.258 14975 Z= 0.335 Chirality : 0.043 0.250 1667 Planarity : 0.004 0.049 1909 Dihedral : 4.639 31.338 1514 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 1.76 % 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: -1.02 (0.24), residues: 1349 helix: 0.53 (0.25), residues: 442 sheet: -1.15 (0.28), residues: 342 loop : -1.24 (0.28), residues: 565 *********************** 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 207 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.263 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 202 average time/residue: 0.2211 time to fit residues: 64.5920 Evaluate side-chains 176 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0940 time to fit residues: 2.7618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 88 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11040 Z= 0.195 Angle : 0.670 10.637 14975 Z= 0.333 Chirality : 0.043 0.186 1667 Planarity : 0.004 0.049 1909 Dihedral : 4.533 31.159 1514 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.32 % 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: -0.88 (0.24), residues: 1349 helix: 0.72 (0.25), residues: 437 sheet: -1.13 (0.28), residues: 343 loop : -1.16 (0.28), residues: 569 *********************** 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 196 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 189 average time/residue: 0.2255 time to fit residues: 62.2027 Evaluate side-chains 174 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1130 time to fit residues: 3.5510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.0170 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- 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 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11040 Z= 0.197 Angle : 0.676 10.160 14975 Z= 0.335 Chirality : 0.043 0.255 1667 Planarity : 0.004 0.048 1909 Dihedral : 4.509 30.313 1514 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.62 % 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: 0.71 (0.25), residues: 437 sheet: -1.14 (0.28), residues: 334 loop : -1.11 (0.28), residues: 578 *********************** 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 181 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 1.285 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 177 average time/residue: 0.2264 time to fit residues: 57.8031 Evaluate side-chains 170 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1049 time to fit residues: 2.6183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11040 Z= 0.188 Angle : 0.670 10.202 14975 Z= 0.334 Chirality : 0.043 0.257 1667 Planarity : 0.004 0.047 1909 Dihedral : 4.461 31.136 1514 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.62 % 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: -0.78 (0.24), residues: 1349 helix: 0.75 (0.25), residues: 443 sheet: -1.06 (0.28), residues: 332 loop : -1.09 (0.28), residues: 574 ********************** 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 185 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 182 average time/residue: 0.2309 time to fit residues: 60.7015 Evaluate side-chains 168 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1208 time to fit residues: 2.3216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.0970 chunk 32 optimal weight: 0.0970 chunk 98 optimal weight: 10.0000 chunk 15 optimal weight: 0.0270 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.6438 ------------------------------------------------------------------------------- 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 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.095039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075144 restraints weight = 33804.845| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.05 r_work: 0.3321 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11040 Z= 0.236 Angle : 0.703 10.380 14975 Z= 0.349 Chirality : 0.044 0.233 1667 Planarity : 0.004 0.048 1909 Dihedral : 4.553 31.033 1514 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.44 % 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: -0.79 (0.24), residues: 1349 helix: 0.79 (0.25), residues: 443 sheet: -1.08 (0.28), residues: 331 loop : -1.13 (0.28), residues: 575 =============================================================================== Job complete usr+sys time: 2534.07 seconds wall clock time: 47 minutes 10.24 seconds (2830.24 seconds total)