Starting phenix.real_space_refine on Sun Apr 7 01:42:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2024/6uus_20901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2024/6uus_20901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2024/6uus_20901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2024/6uus_20901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2024/6uus_20901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uus_20901/04_2024/6uus_20901.pdb" } resolution = 2.4 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= 0.003 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 65 5.16 5 C 5929 2.51 5 N 1624 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 35": "OD1" <-> "OD2" Residue "P ASP 39": "OD1" <-> "OD2" Residue "P ARG 44": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ASP 90": "OD1" <-> "OD2" Residue "R PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 113": "NH1" <-> "NH2" Residue "R PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 233": "OE1" <-> "OE2" Residue "R TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 274": "NH1" <-> "NH2" Residue "R TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 280": "OD1" <-> "OD2" Residue "R ARG 314": "NH1" <-> "NH2" Residue "R GLU 348": "OE1" <-> "OE2" Residue "R TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 366": "OD1" <-> "OD2" Residue "R PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 390": "OE1" <-> "OE2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9308 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "R" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2734 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 8, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 749 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 5.07, per 1000 atoms: 0.54 Number of scatterers: 9308 At special positions: 0 Unit cell: (129.48, 98.77, 130.31, 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 65 16.00 O 1690 8.00 N 1624 7.00 C 5929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 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 P 16 " - pdb=" SG CYS P 21 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.04 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 39.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 removed outlier: 3.592A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.520A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.565A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.622A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 4.161A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.646A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 33 Processing helix chain 'R' and resid 36 through 52 Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 133 through 166 Processing helix chain 'R' and resid 171 through 198 Processing helix chain 'R' and resid 201 through 208 removed outlier: 4.049A pdb=" N VAL R 205 " --> pdb=" O ASN R 201 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 241 removed outlier: 4.398A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 removed outlier: 3.551A pdb=" N TYR R 256 " --> pdb=" O LEU R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 278 Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 320 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 346 removed outlier: 3.783A pdb=" N THR R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 364 through 375 Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 399 Processing helix chain 'E' and resid 36 through 48 removed outlier: 4.068A pdb=" N CYS E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 77 removed outlier: 4.065A pdb=" N PHE E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 99 removed outlier: 4.234A pdb=" N THR E 94 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 143 Proline residue: E 126 - end of helix removed outlier: 3.861A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.400A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.578A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.677A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.676A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.555A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.216A 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: 6.847A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.324A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.678A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.048A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 68 through 69 removed outlier: 3.875A pdb=" N THR R 68 " --> pdb=" O TRP R 75 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP R 75 " --> pdb=" O THR R 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 82 through 83 437 hydrogen bonds defined for protein. 1248 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: 2.56 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3037 1.34 - 1.46: 2331 1.46 - 1.58: 4059 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 9514 Sorted by residual: bond pdb=" CA VAL R 342 " pdb=" CB VAL R 342 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.63e+00 bond pdb=" C ALA B 287 " pdb=" N GLY B 288 " ideal model delta sigma weight residual 1.332 1.325 0.007 6.60e-03 2.30e+04 1.04e+00 bond pdb=" C TRP E 84 " pdb=" N PRO E 85 " ideal model delta sigma weight residual 1.334 1.353 -0.020 2.34e-02 1.83e+03 6.95e-01 bond pdb=" NE ARG R 67 " pdb=" CZ ARG R 67 " ideal model delta sigma weight residual 1.326 1.335 -0.009 1.10e-02 8.26e+03 6.48e-01 bond pdb=" CA ASP E 116 " pdb=" CB ASP E 116 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.94e-01 ... (remaining 9509 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.12: 230 107.12 - 113.84: 5280 113.84 - 120.57: 3797 120.57 - 127.29: 3489 127.29 - 134.02: 113 Bond angle restraints: 12909 Sorted by residual: angle pdb=" C PRO E 115 " pdb=" N ASP E 116 " pdb=" CA ASP E 116 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C ARG E 36 " pdb=" N LEU E 37 " pdb=" CA LEU E 37 " ideal model delta sigma weight residual 120.06 123.74 -3.68 1.19e+00 7.06e-01 9.59e+00 angle pdb=" CA LEU E 37 " pdb=" C LEU E 37 " pdb=" N PRO E 38 " ideal model delta sigma weight residual 121.08 118.09 2.99 1.08e+00 8.57e-01 7.68e+00 angle pdb=" N GLY B 306 " pdb=" CA GLY B 306 " pdb=" C GLY B 306 " ideal model delta sigma weight residual 110.38 114.08 -3.70 1.48e+00 4.57e-01 6.27e+00 angle pdb=" CA LEU E 37 " pdb=" C LEU E 37 " pdb=" O LEU E 37 " ideal model delta sigma weight residual 117.98 120.32 -2.34 9.70e-01 1.06e+00 5.84e+00 ... (remaining 12904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4882 17.97 - 35.94: 515 35.94 - 53.91: 181 53.91 - 71.87: 33 71.87 - 89.84: 10 Dihedral angle restraints: 5621 sinusoidal: 2158 harmonic: 3463 Sorted by residual: dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 127 " pdb=" CB CYS R 127 " ideal model delta sinusoidal sigma weight residual 93.00 47.73 45.27 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CA TYR R 49 " pdb=" C TYR R 49 " pdb=" N GLN R 50 " pdb=" CA GLN R 50 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual -86.00 -51.60 -34.40 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 5618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 852 0.027 - 0.053: 360 0.053 - 0.080: 146 0.080 - 0.107: 63 0.107 - 0.133: 28 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1446 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 114 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO E 115 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 115 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 115 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO E 114 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 125 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO E 126 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 126 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 126 " -0.018 5.00e-02 4.00e+02 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1025 2.75 - 3.29: 9125 3.29 - 3.83: 15893 3.83 - 4.36: 18868 4.36 - 4.90: 32023 Nonbonded interactions: 76934 Sorted by model distance: nonbonded pdb=" O ASN R 187 " pdb=" OG1 THR R 191 " model vdw 2.214 2.440 nonbonded pdb=" OD2 ASP A 229 " pdb=" OG SER N 112 " model vdw 2.218 2.440 nonbonded pdb=" OD2 ASP R 70 " pdb=" OH TYR R 124 " model vdw 2.223 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.274 2.440 nonbonded pdb=" O THR R 102 " pdb=" OG1 THR R 122 " model vdw 2.294 2.440 ... (remaining 76929 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.440 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.050 Find NCS groups from input model: 0.240 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 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 : 0.002 0.020 9514 Z= 0.129 Angle : 0.501 7.555 12909 Z= 0.297 Chirality : 0.039 0.133 1449 Planarity : 0.003 0.042 1646 Dihedral : 17.128 89.842 3350 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.27 % Allowed : 23.70 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.22), residues: 1160 helix: -1.09 (0.23), residues: 433 sheet: -1.53 (0.30), residues: 222 loop : -1.71 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 229 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE E 100 TYR 0.015 0.001 TYR N 60 ARG 0.008 0.001 ARG R 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7782 (ttpt) cc_final: 0.7560 (tttm) REVERT: A 347 ARG cc_start: 0.7320 (ttp80) cc_final: 0.7031 (ttp-110) REVERT: A 390 GLN cc_start: 0.7441 (mt0) cc_final: 0.7211 (mt0) REVERT: B 46 ARG cc_start: 0.7485 (mpt180) cc_final: 0.7169 (mmt90) REVERT: B 66 ASP cc_start: 0.7106 (p0) cc_final: 0.6764 (p0) REVERT: B 219 ARG cc_start: 0.6877 (mmt90) cc_final: 0.6479 (mpt-90) REVERT: B 259 GLN cc_start: 0.6538 (tt0) cc_final: 0.6231 (tt0) REVERT: B 322 ASP cc_start: 0.6030 (m-30) cc_final: 0.5659 (m-30) REVERT: G 21 MET cc_start: 0.5795 (tpt) cc_final: 0.5548 (mmt) REVERT: G 47 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: N 95 TYR cc_start: 0.7406 (m-80) cc_final: 0.7142 (m-80) REVERT: N 105 ARG cc_start: 0.6112 (mtp180) cc_final: 0.5901 (mtm180) REVERT: N 108 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.5484 (t80) REVERT: R 139 LEU cc_start: 0.6452 (mm) cc_final: 0.6217 (mt) REVERT: R 147 ILE cc_start: 0.6784 (tt) cc_final: 0.6279 (mm) REVERT: R 276 LEU cc_start: 0.7726 (mt) cc_final: 0.6621 (tp) REVERT: R 321 LYS cc_start: 0.5920 (mmtm) cc_final: 0.5702 (mmtp) REVERT: R 332 MET cc_start: 0.5105 (tpt) cc_final: 0.4318 (ttm) REVERT: R 370 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5227 (t-90) REVERT: R 396 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.4241 (mtp85) REVERT: E 64 VAL cc_start: 0.3525 (OUTLIER) cc_final: 0.3190 (t) outliers start: 32 outliers final: 9 residues processed: 171 average time/residue: 1.2349 time to fit residues: 225.6340 Evaluate side-chains 137 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 370 HIS Chi-restraints excluded: chain R residue 396 ARG Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 239 ASN B 268 ASN B 311 HIS N 1 GLN N 31 ASN P 50 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 388 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9514 Z= 0.207 Angle : 0.551 7.505 12909 Z= 0.299 Chirality : 0.042 0.142 1449 Planarity : 0.004 0.046 1646 Dihedral : 6.343 72.730 1308 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.47 % Allowed : 24.00 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1160 helix: 0.39 (0.24), residues: 444 sheet: -1.13 (0.32), residues: 219 loop : -1.28 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.007 0.001 HIS R 374 PHE 0.019 0.002 PHE A 212 TYR 0.012 0.001 TYR N 80 ARG 0.006 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7230 (tt0) cc_final: 0.6953 (tt0) REVERT: A 28 LYS cc_start: 0.7762 (ttpt) cc_final: 0.6908 (mmpt) REVERT: A 347 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7287 (ttp80) REVERT: B 44 GLN cc_start: 0.7137 (mt0) cc_final: 0.6700 (mt0) REVERT: B 46 ARG cc_start: 0.7513 (mpt180) cc_final: 0.7135 (mmt90) REVERT: B 59 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7440 (t80) REVERT: B 66 ASP cc_start: 0.7416 (p0) cc_final: 0.7033 (p0) REVERT: B 76 ASP cc_start: 0.8035 (p0) cc_final: 0.7791 (p0) REVERT: B 219 ARG cc_start: 0.6982 (mmt90) cc_final: 0.6700 (mpt-90) REVERT: B 259 GLN cc_start: 0.6668 (tt0) cc_final: 0.6454 (tt0) REVERT: B 322 ASP cc_start: 0.6174 (m-30) cc_final: 0.5847 (m-30) REVERT: G 21 MET cc_start: 0.5780 (tpt) cc_final: 0.5317 (mmt) REVERT: P 50 GLN cc_start: 0.2150 (OUTLIER) cc_final: 0.1337 (tm-30) REVERT: R 48 CYS cc_start: 0.4023 (OUTLIER) cc_final: 0.2255 (t) REVERT: R 126 GLN cc_start: 0.3958 (OUTLIER) cc_final: 0.3753 (pm20) REVERT: R 169 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4745 (mt) REVERT: R 314 ARG cc_start: 0.6909 (ttp80) cc_final: 0.6549 (ttp-170) REVERT: R 321 LYS cc_start: 0.6071 (mmtm) cc_final: 0.5792 (mmtp) REVERT: R 332 MET cc_start: 0.5244 (tpt) cc_final: 0.4513 (ttm) REVERT: R 375 PHE cc_start: 0.7943 (m-80) cc_final: 0.7688 (m-80) REVERT: E 64 VAL cc_start: 0.3556 (OUTLIER) cc_final: 0.3188 (t) outliers start: 34 outliers final: 10 residues processed: 151 average time/residue: 1.2235 time to fit residues: 198.0735 Evaluate side-chains 132 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 126 GLN Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 0.0270 chunk 114 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 268 ASN N 1 GLN N 31 ASN N 53 GLN P 50 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9514 Z= 0.150 Angle : 0.489 7.194 12909 Z= 0.264 Chirality : 0.041 0.139 1449 Planarity : 0.004 0.045 1646 Dihedral : 4.924 58.522 1294 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.17 % Allowed : 24.31 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1160 helix: 1.21 (0.25), residues: 443 sheet: -0.71 (0.33), residues: 218 loop : -0.93 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS R 374 PHE 0.015 0.001 PHE R 182 TYR 0.009 0.001 TYR R 46 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7150 (tt0) cc_final: 0.6920 (tt0) REVERT: A 21 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6288 (tm-30) REVERT: A 28 LYS cc_start: 0.7768 (ttpt) cc_final: 0.6939 (mmpt) REVERT: A 34 LYS cc_start: 0.7949 (ttpp) cc_final: 0.7704 (tttp) REVERT: A 347 ARG cc_start: 0.7440 (ttp80) cc_final: 0.7162 (ttp-110) REVERT: A 389 ARG cc_start: 0.7353 (tpp-160) cc_final: 0.7017 (ttt-90) REVERT: B 44 GLN cc_start: 0.7164 (mt0) cc_final: 0.6951 (mt0) REVERT: B 46 ARG cc_start: 0.7515 (mpt180) cc_final: 0.7135 (mmt90) REVERT: B 59 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7519 (t80) REVERT: B 66 ASP cc_start: 0.7429 (p0) cc_final: 0.7065 (p0) REVERT: B 76 ASP cc_start: 0.8037 (p0) cc_final: 0.7788 (p0) REVERT: B 219 ARG cc_start: 0.6951 (mmt90) cc_final: 0.6676 (mpt-90) REVERT: B 322 ASP cc_start: 0.6192 (m-30) cc_final: 0.5891 (m-30) REVERT: G 21 MET cc_start: 0.5710 (tpt) cc_final: 0.5233 (mmt) REVERT: N 43 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7081 (mtmt) REVERT: P 50 GLN cc_start: 0.1525 (OUTLIER) cc_final: 0.0531 (tp-100) REVERT: R 48 CYS cc_start: 0.3954 (OUTLIER) cc_final: 0.1654 (t) REVERT: R 74 CYS cc_start: 0.2123 (OUTLIER) cc_final: 0.0830 (p) REVERT: R 143 TYR cc_start: 0.6503 (m-10) cc_final: 0.6278 (m-10) REVERT: R 169 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4839 (mt) REVERT: R 250 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6724 (mt0) REVERT: R 321 LYS cc_start: 0.6018 (mmtm) cc_final: 0.5747 (mmtp) REVERT: R 332 MET cc_start: 0.5162 (tpt) cc_final: 0.4563 (ttm) REVERT: E 64 VAL cc_start: 0.3541 (OUTLIER) cc_final: 0.3199 (t) REVERT: E 136 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7193 (tp) REVERT: E 142 LYS cc_start: 0.5602 (ttpp) cc_final: 0.4908 (tttt) outliers start: 31 outliers final: 8 residues processed: 140 average time/residue: 1.2861 time to fit residues: 192.5497 Evaluate side-chains 126 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 31 ASN N 53 GLN P 50 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9514 Z= 0.147 Angle : 0.480 7.300 12909 Z= 0.259 Chirality : 0.041 0.139 1449 Planarity : 0.004 0.044 1646 Dihedral : 4.746 59.597 1291 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.78 % Allowed : 24.41 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1160 helix: 1.59 (0.25), residues: 438 sheet: -0.48 (0.33), residues: 218 loop : -0.78 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS R 374 PHE 0.015 0.001 PHE E 100 TYR 0.022 0.001 TYR N 60 ARG 0.008 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6262 (tm-30) REVERT: A 28 LYS cc_start: 0.7788 (ttpt) cc_final: 0.6991 (mmpt) REVERT: A 347 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7188 (ttp-110) REVERT: B 5 ASP cc_start: 0.3360 (OUTLIER) cc_final: 0.2642 (p0) REVERT: B 46 ARG cc_start: 0.7522 (mpt180) cc_final: 0.7132 (mmt90) REVERT: B 59 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7463 (t80) REVERT: B 66 ASP cc_start: 0.7324 (p0) cc_final: 0.6983 (p0) REVERT: B 76 ASP cc_start: 0.8094 (p0) cc_final: 0.7814 (p0) REVERT: B 219 ARG cc_start: 0.6917 (mmt90) cc_final: 0.6647 (mpt-90) REVERT: B 322 ASP cc_start: 0.6143 (m-30) cc_final: 0.5839 (m-30) REVERT: G 21 MET cc_start: 0.5754 (tpt) cc_final: 0.5237 (mmt) REVERT: N 43 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7110 (mtmt) REVERT: P 50 GLN cc_start: 0.1521 (OUTLIER) cc_final: 0.0471 (tp-100) REVERT: R 48 CYS cc_start: 0.4155 (OUTLIER) cc_final: 0.2266 (t) REVERT: R 143 TYR cc_start: 0.6415 (m-10) cc_final: 0.6173 (m-10) REVERT: R 169 LEU cc_start: 0.5159 (OUTLIER) cc_final: 0.4851 (mt) REVERT: R 250 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6963 (mt0) REVERT: R 314 ARG cc_start: 0.6967 (ttp80) cc_final: 0.6569 (tmm160) REVERT: R 321 LYS cc_start: 0.6062 (mmtm) cc_final: 0.5795 (mmtp) REVERT: R 332 MET cc_start: 0.5037 (tpt) cc_final: 0.4585 (ttm) REVERT: E 64 VAL cc_start: 0.3544 (OUTLIER) cc_final: 0.3196 (t) REVERT: E 93 ILE cc_start: 0.3692 (OUTLIER) cc_final: 0.3429 (pp) REVERT: E 136 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7190 (tp) REVERT: E 142 LYS cc_start: 0.5642 (ttpp) cc_final: 0.4951 (tttt) outliers start: 37 outliers final: 14 residues processed: 145 average time/residue: 1.2526 time to fit residues: 194.1658 Evaluate side-chains 132 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN P 50 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 ASN ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9514 Z= 0.357 Angle : 0.686 9.322 12909 Z= 0.371 Chirality : 0.048 0.151 1449 Planarity : 0.005 0.047 1646 Dihedral : 5.714 56.676 1291 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.01 % Allowed : 22.68 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1160 helix: 1.03 (0.24), residues: 442 sheet: -0.61 (0.31), residues: 226 loop : -0.93 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 234 HIS 0.008 0.002 HIS R 149 PHE 0.018 0.003 PHE R 228 TYR 0.022 0.002 TYR N 60 ARG 0.010 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 118 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6630 (tttm) REVERT: A 28 LYS cc_start: 0.7745 (ttpt) cc_final: 0.6984 (mmpt) REVERT: A 35 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7094 (mm-40) REVERT: A 327 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5243 (mp0) REVERT: A 347 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7173 (ttp-110) REVERT: B 5 ASP cc_start: 0.3840 (OUTLIER) cc_final: 0.2951 (p0) REVERT: B 46 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7156 (mmt90) REVERT: B 66 ASP cc_start: 0.7325 (p0) cc_final: 0.6927 (p0) REVERT: B 219 ARG cc_start: 0.6958 (mmt90) cc_final: 0.6741 (mpt-90) REVERT: B 322 ASP cc_start: 0.6501 (m-30) cc_final: 0.6248 (m-30) REVERT: G 21 MET cc_start: 0.5857 (tpt) cc_final: 0.5354 (mmt) REVERT: N 65 LYS cc_start: 0.6940 (ttmt) cc_final: 0.6441 (ttpt) REVERT: P 50 GLN cc_start: 0.1259 (OUTLIER) cc_final: 0.0166 (tp-100) REVERT: R 136 LYS cc_start: 0.5073 (OUTLIER) cc_final: 0.4686 (ttmt) REVERT: R 250 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: R 252 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7080 (mt) REVERT: R 314 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6666 (ttp-170) REVERT: R 321 LYS cc_start: 0.6197 (mmtm) cc_final: 0.5891 (mmtp) REVERT: R 332 MET cc_start: 0.5042 (tpt) cc_final: 0.4652 (ttm) REVERT: R 333 LYS cc_start: 0.5322 (mmtt) cc_final: 0.5049 (mmmm) REVERT: R 375 PHE cc_start: 0.7809 (m-80) cc_final: 0.7557 (m-80) outliers start: 49 outliers final: 22 residues processed: 155 average time/residue: 1.1984 time to fit residues: 199.0523 Evaluate side-chains 137 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 GLN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9514 Z= 0.208 Angle : 0.569 9.894 12909 Z= 0.305 Chirality : 0.043 0.145 1449 Planarity : 0.004 0.046 1646 Dihedral : 5.401 58.315 1291 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.19 % Allowed : 24.72 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1160 helix: 1.34 (0.25), residues: 444 sheet: -0.60 (0.32), residues: 224 loop : -0.84 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.010 0.001 HIS A 220 PHE 0.017 0.002 PHE E 100 TYR 0.019 0.001 TYR N 60 ARG 0.006 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 112 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6311 (tm-30) REVERT: A 28 LYS cc_start: 0.7750 (ttpt) cc_final: 0.6986 (mmpt) REVERT: A 34 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7725 (tttp) REVERT: A 216 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6469 (mmpt) REVERT: A 327 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.5277 (mp0) REVERT: A 347 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7132 (ttp-110) REVERT: B 5 ASP cc_start: 0.3838 (OUTLIER) cc_final: 0.2970 (p0) REVERT: B 44 GLN cc_start: 0.7203 (mp10) cc_final: 0.6821 (mt0) REVERT: B 46 ARG cc_start: 0.7548 (mpt180) cc_final: 0.7145 (mmt90) REVERT: B 59 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7402 (t80) REVERT: B 76 ASP cc_start: 0.8076 (p0) cc_final: 0.7844 (p0) REVERT: B 146 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8027 (mm) REVERT: B 219 ARG cc_start: 0.6925 (mmt90) cc_final: 0.6628 (mpt-90) REVERT: B 322 ASP cc_start: 0.6472 (m-30) cc_final: 0.6195 (m-30) REVERT: N 43 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7363 (mttt) REVERT: N 61 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7326 (t) REVERT: N 65 LYS cc_start: 0.6854 (ttmt) cc_final: 0.6368 (ttpt) REVERT: R 48 CYS cc_start: 0.4293 (OUTLIER) cc_final: 0.2124 (t) REVERT: R 49 TYR cc_start: 0.4621 (OUTLIER) cc_final: 0.3948 (t80) REVERT: R 169 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5437 (mp) REVERT: R 314 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6677 (tmm160) REVERT: R 321 LYS cc_start: 0.6187 (mmtm) cc_final: 0.5908 (mmtp) REVERT: R 333 LYS cc_start: 0.5293 (mmtt) cc_final: 0.5033 (mmmm) REVERT: R 375 PHE cc_start: 0.7871 (m-80) cc_final: 0.7652 (m-80) REVERT: E 93 ILE cc_start: 0.3851 (OUTLIER) cc_final: 0.3487 (pp) REVERT: E 136 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7213 (tp) outliers start: 41 outliers final: 17 residues processed: 145 average time/residue: 1.2064 time to fit residues: 187.2310 Evaluate side-chains 133 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 GLN Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9514 Z= 0.178 Angle : 0.538 8.686 12909 Z= 0.287 Chirality : 0.042 0.145 1449 Planarity : 0.004 0.044 1646 Dihedral : 5.215 59.281 1291 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.58 % Allowed : 25.54 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.24 (0.25), residues: 1160 helix: 1.52 (0.25), residues: 444 sheet: -0.51 (0.32), residues: 211 loop : -0.73 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.017 0.002 PHE E 100 TYR 0.027 0.001 TYR N 60 ARG 0.005 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6335 (tm-30) REVERT: A 24 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6374 (ttpp) REVERT: A 28 LYS cc_start: 0.7749 (ttpt) cc_final: 0.6988 (mmpt) REVERT: A 34 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7733 (tttp) REVERT: A 216 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6503 (mmpt) REVERT: A 347 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7127 (ttp-110) REVERT: B 5 ASP cc_start: 0.3990 (OUTLIER) cc_final: 0.3150 (p0) REVERT: B 25 CYS cc_start: 0.5698 (OUTLIER) cc_final: 0.5175 (t) REVERT: B 44 GLN cc_start: 0.7194 (mp10) cc_final: 0.6864 (mt0) REVERT: B 46 ARG cc_start: 0.7546 (mpt180) cc_final: 0.7155 (mmt90) REVERT: B 59 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 76 ASP cc_start: 0.8077 (p0) cc_final: 0.7819 (p0) REVERT: B 188 MET cc_start: 0.7981 (mmm) cc_final: 0.7686 (mmm) REVERT: B 219 ARG cc_start: 0.6928 (mmt90) cc_final: 0.6616 (mpt-90) REVERT: B 322 ASP cc_start: 0.6440 (m-30) cc_final: 0.6176 (m-30) REVERT: N 43 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7264 (mttt) REVERT: N 65 LYS cc_start: 0.6842 (ttmt) cc_final: 0.6383 (ttpt) REVERT: R 49 TYR cc_start: 0.4687 (OUTLIER) cc_final: 0.4092 (t80) REVERT: R 169 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5374 (mt) REVERT: R 252 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6272 (mp) REVERT: R 314 ARG cc_start: 0.6952 (ttp80) cc_final: 0.6658 (tmm160) REVERT: R 321 LYS cc_start: 0.6159 (mmtm) cc_final: 0.5895 (mmtp) REVERT: R 333 LYS cc_start: 0.5243 (mmtt) cc_final: 0.4931 (mmmm) REVERT: E 93 ILE cc_start: 0.3791 (OUTLIER) cc_final: 0.3421 (pp) outliers start: 35 outliers final: 16 residues processed: 139 average time/residue: 1.2972 time to fit residues: 192.7839 Evaluate side-chains 131 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 41 HIS B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9514 Z= 0.292 Angle : 0.640 9.552 12909 Z= 0.344 Chirality : 0.046 0.154 1449 Planarity : 0.005 0.046 1646 Dihedral : 5.636 56.688 1291 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.29 % Allowed : 24.11 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1160 helix: 1.16 (0.25), residues: 446 sheet: -0.53 (0.31), residues: 226 loop : -0.81 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.011 0.002 HIS R 374 PHE 0.018 0.002 PHE R 92 TYR 0.023 0.002 TYR N 60 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6348 (ttpp) REVERT: A 28 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7002 (mmpt) REVERT: A 34 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7744 (tttp) REVERT: A 216 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6467 (mmpt) REVERT: A 327 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.5078 (mp0) REVERT: A 347 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7151 (ttp-110) REVERT: B 5 ASP cc_start: 0.3685 (OUTLIER) cc_final: 0.2875 (p0) REVERT: B 44 GLN cc_start: 0.7223 (mt0) cc_final: 0.6842 (mt0) REVERT: B 45 MET cc_start: 0.7482 (ttp) cc_final: 0.6884 (ttp) REVERT: B 46 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7157 (mmt90) REVERT: B 137 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7266 (ttm-80) REVERT: B 219 ARG cc_start: 0.6942 (mmt90) cc_final: 0.6628 (mpt-90) REVERT: B 322 ASP cc_start: 0.6480 (m-30) cc_final: 0.6234 (m-30) REVERT: N 43 LYS cc_start: 0.7723 (mtpp) cc_final: 0.7337 (mttt) REVERT: N 61 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7378 (t) REVERT: N 65 LYS cc_start: 0.6910 (ttmt) cc_final: 0.6116 (ttmt) REVERT: R 49 TYR cc_start: 0.4741 (OUTLIER) cc_final: 0.4020 (t80) REVERT: R 165 TYR cc_start: 0.6069 (t80) cc_final: 0.5655 (t80) REVERT: R 169 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5543 (mt) REVERT: R 314 ARG cc_start: 0.6997 (ttp80) cc_final: 0.6636 (ttp-170) REVERT: R 333 LYS cc_start: 0.5213 (mmtt) cc_final: 0.4917 (mmmm) REVERT: E 93 ILE cc_start: 0.3857 (OUTLIER) cc_final: 0.3483 (pp) outliers start: 42 outliers final: 21 residues processed: 140 average time/residue: 1.2427 time to fit residues: 186.6356 Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9514 Z= 0.208 Angle : 0.568 8.558 12909 Z= 0.304 Chirality : 0.043 0.152 1449 Planarity : 0.004 0.045 1646 Dihedral : 5.390 58.242 1291 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.37 % Allowed : 25.33 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.15 (0.24), residues: 1160 helix: 1.37 (0.25), residues: 450 sheet: -0.55 (0.32), residues: 216 loop : -0.72 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.009 0.001 HIS R 374 PHE 0.017 0.002 PHE E 100 TYR 0.021 0.001 TYR N 60 ARG 0.006 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6313 (tm-30) REVERT: A 24 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6295 (ttpp) REVERT: A 28 LYS cc_start: 0.7750 (ttpt) cc_final: 0.6982 (mmpt) REVERT: A 216 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6510 (mmpt) REVERT: A 327 GLU cc_start: 0.5472 (OUTLIER) cc_final: 0.5115 (mp0) REVERT: A 347 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7188 (ttp80) REVERT: B 5 ASP cc_start: 0.3715 (OUTLIER) cc_final: 0.2936 (p0) REVERT: B 44 GLN cc_start: 0.7172 (mt0) cc_final: 0.6833 (mt0) REVERT: B 45 MET cc_start: 0.7422 (ttp) cc_final: 0.6895 (ttp) REVERT: B 46 ARG cc_start: 0.7532 (mpt180) cc_final: 0.7104 (mmt90) REVERT: B 59 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7383 (t80) REVERT: B 219 ARG cc_start: 0.6929 (mmt90) cc_final: 0.6605 (mpt-90) REVERT: B 322 ASP cc_start: 0.6452 (m-30) cc_final: 0.6196 (m-30) REVERT: N 43 LYS cc_start: 0.7641 (mtpp) cc_final: 0.7251 (mttt) REVERT: N 61 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7357 (t) REVERT: N 65 LYS cc_start: 0.6907 (ttmt) cc_final: 0.6419 (ttpt) REVERT: R 165 TYR cc_start: 0.6059 (t80) cc_final: 0.5634 (t80) REVERT: R 169 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5476 (mt) REVERT: R 314 ARG cc_start: 0.6972 (ttp80) cc_final: 0.6683 (tmm160) REVERT: R 333 LYS cc_start: 0.5123 (mmtt) cc_final: 0.4785 (mmmm) REVERT: E 93 ILE cc_start: 0.3806 (OUTLIER) cc_final: 0.3550 (pp) outliers start: 33 outliers final: 19 residues processed: 137 average time/residue: 1.3059 time to fit residues: 191.2229 Evaluate side-chains 129 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9514 Z= 0.225 Angle : 0.586 10.172 12909 Z= 0.313 Chirality : 0.044 0.150 1449 Planarity : 0.004 0.045 1646 Dihedral : 5.408 58.304 1291 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.17 % Allowed : 25.54 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1160 helix: 1.39 (0.25), residues: 446 sheet: -0.48 (0.31), residues: 226 loop : -0.75 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.009 0.001 HIS R 374 PHE 0.017 0.002 PHE E 100 TYR 0.021 0.002 TYR N 60 ARG 0.006 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6348 (ttpp) REVERT: A 28 LYS cc_start: 0.7749 (ttpt) cc_final: 0.6999 (mmpt) REVERT: A 216 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6516 (mmpt) REVERT: A 327 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5176 (mp0) REVERT: A 347 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7137 (ttp-110) REVERT: B 5 ASP cc_start: 0.3677 (OUTLIER) cc_final: 0.2925 (p0) REVERT: B 44 GLN cc_start: 0.7160 (mt0) cc_final: 0.6809 (mt0) REVERT: B 45 MET cc_start: 0.7449 (ttp) cc_final: 0.6927 (ttp) REVERT: B 46 ARG cc_start: 0.7527 (mpt180) cc_final: 0.7090 (mmt90) REVERT: B 219 ARG cc_start: 0.6930 (mmt90) cc_final: 0.6599 (mpt-90) REVERT: B 322 ASP cc_start: 0.6463 (m-30) cc_final: 0.6206 (m-30) REVERT: N 43 LYS cc_start: 0.7638 (mtpp) cc_final: 0.7239 (mttt) REVERT: N 61 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7431 (t) REVERT: N 65 LYS cc_start: 0.6903 (ttmt) cc_final: 0.6412 (ttpt) REVERT: R 114 HIS cc_start: 0.1790 (OUTLIER) cc_final: 0.1421 (t-90) REVERT: R 165 TYR cc_start: 0.6052 (t80) cc_final: 0.5630 (t80) REVERT: R 314 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6614 (ttp-170) REVERT: R 332 MET cc_start: 0.5951 (tmm) cc_final: 0.4739 (ptt) REVERT: R 333 LYS cc_start: 0.5135 (mmtt) cc_final: 0.4878 (mmmm) REVERT: E 93 ILE cc_start: 0.3827 (OUTLIER) cc_final: 0.3557 (pp) outliers start: 31 outliers final: 23 residues processed: 127 average time/residue: 1.2546 time to fit residues: 170.9382 Evaluate side-chains 131 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 29 GLN Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.203486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161738 restraints weight = 9615.155| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.80 r_work: 0.3639 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9514 Z= 0.176 Angle : 0.543 9.742 12909 Z= 0.289 Chirality : 0.042 0.146 1449 Planarity : 0.004 0.045 1646 Dihedral : 5.217 59.713 1291 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.17 % Allowed : 25.74 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.37 (0.25), residues: 1160 helix: 1.68 (0.25), residues: 440 sheet: -0.35 (0.32), residues: 219 loop : -0.73 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS R 374 PHE 0.017 0.002 PHE E 100 TYR 0.021 0.001 TYR N 60 ARG 0.005 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4012.12 seconds wall clock time: 72 minutes 28.02 seconds (4348.02 seconds total)