Starting phenix.real_space_refine on Wed Feb 14 07:44:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oij_20078/02_2024/6oij_20078.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oij_20078/02_2024/6oij_20078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oij_20078/02_2024/6oij_20078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oij_20078/02_2024/6oij_20078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oij_20078/02_2024/6oij_20078.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oij_20078/02_2024/6oij_20078.pdb" } resolution = 3.3 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= 0.004 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 59 5.16 5 C 5697 2.51 5 N 1500 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "R TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R ARG 129": "NH1" <-> "NH2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 210": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "R GLU 214": "OE1" <-> "OE2" Residue "R ARG 218": "NH1" <-> "NH2" Residue "R PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 426": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8877 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1781 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2273 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "H" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1757 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 421 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'IXO': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.10, per 1000 atoms: 0.57 Number of scatterers: 8877 At special positions: 0 Unit cell: (106, 117.66, 107.06, 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 59 16.00 O 1621 8.00 N 1500 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 394 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 6 through 37 removed outlier: 3.835A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 217 removed outlier: 4.072A pdb=" N TRP A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.573A pdb=" N GLU A 221 " --> pdb=" O HIS A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 336 through 356 Processing helix chain 'R' and resid 23 through 53 Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.852A pdb=" N TYR R 62 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU R 64 " --> pdb=" O ASN R 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 89 removed outlier: 3.543A pdb=" N MET R 88 " --> pdb=" O THR R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 168 removed outlier: 4.011A pdb=" N SER R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Proline residue: R 159 - end of helix removed outlier: 3.508A pdb=" N LEU R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 184 removed outlier: 4.126A pdb=" N LEU R 183 " --> pdb=" O ILE R 180 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER R 184 " --> pdb=" O GLN R 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 180 through 184' Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.577A pdb=" N THR R 189 " --> pdb=" O GLN R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 226 removed outlier: 4.413A pdb=" N ARG R 220 " --> pdb=" O GLU R 216 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU R 221 " --> pdb=" O ASN R 217 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 389 removed outlier: 3.910A pdb=" N ARG R 365 " --> pdb=" O LYS R 361 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 397 through 414 removed outlier: 4.258A pdb=" N CYS R 407 " --> pdb=" O GLY R 403 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR R 408 " --> pdb=" O TYR R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 419 removed outlier: 3.799A pdb=" N TYR R 418 " --> pdb=" O ASN R 414 " (cutoff:3.500A) Processing helix chain 'R' and resid 422 through 432 Processing helix chain 'R' and resid 438 through 442 removed outlier: 3.542A pdb=" N TRP R 442 " --> pdb=" O LYS R 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 22 removed outlier: 4.391A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196 removed outlier: 5.871A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 229 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AA6, first strand: chain 'H' and resid 194 through 195 removed outlier: 6.850A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.790A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.883A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.276A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.718A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.525A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.984A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.640A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1299 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: 2.88 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1409 1.31 - 1.44: 2541 1.44 - 1.56: 5037 1.56 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 9074 Sorted by residual: bond pdb=" C GLU H 234 " pdb=" N TYR H 235 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.07e-02 2.33e+03 1.46e+01 bond pdb=" N11 IXO R 501 " pdb=" O12 IXO R 501 " ideal model delta sigma weight residual 1.385 1.425 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C10 IXO R 501 " pdb=" N11 IXO R 501 " ideal model delta sigma weight residual 1.270 1.310 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C ASP H 74 " pdb=" N PRO H 75 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.61e+00 bond pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.50e+00 ... (remaining 9069 not shown) Histogram of bond angle deviations from ideal: 97.87 - 114.29: 5462 114.29 - 130.70: 6837 130.70 - 147.12: 47 147.12 - 163.53: 0 163.53 - 179.95: 2 Bond angle restraints: 12348 Sorted by residual: angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 122.61 129.80 -7.19 1.56e+00 4.11e-01 2.13e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 108.34 113.73 -5.39 1.31e+00 5.83e-01 1.69e+01 angle pdb=" C TYR R 82 " pdb=" N THR R 83 " pdb=" CA THR R 83 " ideal model delta sigma weight residual 121.14 114.52 6.62 1.75e+00 3.27e-01 1.43e+01 angle pdb=" CA MET H 192 " pdb=" CB MET H 192 " pdb=" CG MET H 192 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" N THR R 379 " pdb=" CA THR R 379 " pdb=" C THR R 379 " ideal model delta sigma weight residual 109.81 117.17 -7.36 2.21e+00 2.05e-01 1.11e+01 ... (remaining 12343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.20: 5080 24.20 - 48.40: 302 48.40 - 72.61: 35 72.61 - 96.81: 6 96.81 - 121.01: 4 Dihedral angle restraints: 5427 sinusoidal: 2083 harmonic: 3344 Sorted by residual: dihedral pdb=" CA GLU A 234 " pdb=" C GLU A 234 " pdb=" N TYR A 235 " pdb=" CA TYR A 235 " ideal model delta harmonic sigma weight residual 180.00 149.44 30.56 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 888 0.044 - 0.089: 368 0.089 - 0.133: 136 0.133 - 0.178: 24 0.178 - 0.222: 8 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE R 180 " pdb=" CA ILE R 180 " pdb=" CG1 ILE R 180 " pdb=" CG2 ILE R 180 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE A 200 " pdb=" CA ILE A 200 " pdb=" CG1 ILE A 200 " pdb=" CG2 ILE A 200 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1421 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 236 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 414 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO R 415 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 415 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 415 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 83 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C THR R 83 " -0.041 2.00e-02 2.50e+03 pdb=" O THR R 83 " 0.015 2.00e-02 2.50e+03 pdb=" N THR R 84 " 0.014 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1689 2.77 - 3.30: 7932 3.30 - 3.83: 14902 3.83 - 4.37: 16879 4.37 - 4.90: 30037 Nonbonded interactions: 71439 Sorted by model distance: nonbonded pdb=" OG1 THR R 377 " pdb=" O LEU R 406 " model vdw 2.236 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.252 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.266 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.280 2.440 nonbonded pdb=" O LEU R 81 " pdb=" OG1 THR R 84 " model vdw 2.287 2.440 ... (remaining 71434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.770 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.790 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.006 0.079 9074 Z= 0.397 Angle : 0.942 11.484 12348 Z= 0.500 Chirality : 0.057 0.222 1424 Planarity : 0.007 0.082 1540 Dihedral : 15.714 121.011 3262 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.77 % Allowed : 12.72 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.70 (0.20), residues: 1134 helix: -2.41 (0.19), residues: 395 sheet: -1.87 (0.30), residues: 238 loop : -2.67 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 91 HIS 0.007 0.002 HIS H 35 PHE 0.022 0.002 PHE R 182 TYR 0.018 0.002 TYR R 404 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 211 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8503 (tptp) cc_final: 0.7979 (ttpt) REVERT: A 357 ASN cc_start: 0.8445 (t0) cc_final: 0.7799 (t0) REVERT: R 404 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6507 (m-10) REVERT: H 5 VAL cc_start: 0.8470 (m) cc_final: 0.8194 (t) REVERT: H 148 PRO cc_start: 0.8548 (Cg_endo) cc_final: 0.8032 (Cg_exo) REVERT: H 192 MET cc_start: 0.8501 (ppp) cc_final: 0.8206 (ppp) REVERT: H 246 GLU cc_start: 0.7377 (mp0) cc_final: 0.7048 (mp0) REVERT: G 48 ASP cc_start: 0.8329 (t0) cc_final: 0.8097 (t0) outliers start: 7 outliers final: 2 residues processed: 214 average time/residue: 0.2214 time to fit residues: 64.0871 Evaluate side-chains 163 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN A 287 HIS R 43 ASN R 61 ASN R 90 HIS R 382 ASN R 410 ASN H 142 GLN H 183 GLN B 75 GLN B 88 ASN B 110 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9074 Z= 0.180 Angle : 0.609 7.832 12348 Z= 0.312 Chirality : 0.042 0.244 1424 Planarity : 0.004 0.066 1540 Dihedral : 7.968 72.698 1403 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.77 % Allowed : 18.69 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1134 helix: -0.18 (0.25), residues: 393 sheet: -1.38 (0.31), residues: 245 loop : -2.15 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS H 167 PHE 0.015 0.001 PHE A 55 TYR 0.015 0.001 TYR R 85 ARG 0.002 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 1.003 Fit side-chains REVERT: A 258 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 294 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7042 (pm20) REVERT: A 311 LYS cc_start: 0.8602 (tptp) cc_final: 0.8134 (ttpt) REVERT: R 217 ASN cc_start: 0.8073 (t0) cc_final: 0.7758 (t0) REVERT: R 404 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: H 11 LEU cc_start: 0.7463 (tp) cc_final: 0.7184 (mp) REVERT: H 18 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6953 (tpt-90) REVERT: H 148 PRO cc_start: 0.8521 (Cg_endo) cc_final: 0.8213 (Cg_exo) REVERT: H 227 TYR cc_start: 0.7881 (m-10) cc_final: 0.7502 (m-80) REVERT: B 19 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.7539 (ttp80) outliers start: 25 outliers final: 14 residues processed: 191 average time/residue: 0.1941 time to fit residues: 52.6008 Evaluate side-chains 167 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 100 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS R 422 ASN H 39 GLN H 142 GLN H 183 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9074 Z= 0.201 Angle : 0.591 7.234 12348 Z= 0.303 Chirality : 0.043 0.214 1424 Planarity : 0.004 0.061 1540 Dihedral : 7.500 79.014 1403 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.54 % Allowed : 20.46 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.24), residues: 1134 helix: 0.69 (0.26), residues: 393 sheet: -1.15 (0.32), residues: 250 loop : -1.93 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS A 287 PHE 0.012 0.001 PHE A 339 TYR 0.013 0.001 TYR H 103 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 221 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 258 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8559 (mt) REVERT: A 294 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7063 (pm20) REVERT: A 311 LYS cc_start: 0.8690 (tptp) cc_final: 0.8152 (ttpt) REVERT: H 18 ARG cc_start: 0.7065 (tpp80) cc_final: 0.6843 (tpt-90) REVERT: H 230 MET cc_start: 0.8011 (tmm) cc_final: 0.7802 (ttp) REVERT: B 19 ARG cc_start: 0.7883 (ttp-170) cc_final: 0.7641 (ttp80) REVERT: G 22 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7409 (mt-10) outliers start: 32 outliers final: 21 residues processed: 190 average time/residue: 0.1993 time to fit residues: 52.7335 Evaluate side-chains 172 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS H 183 GLN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9074 Z= 0.221 Angle : 0.605 8.448 12348 Z= 0.309 Chirality : 0.043 0.214 1424 Planarity : 0.004 0.058 1540 Dihedral : 7.406 82.017 1403 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.54 % Allowed : 21.90 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1134 helix: 0.99 (0.26), residues: 394 sheet: -1.06 (0.32), residues: 245 loop : -1.80 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.005 0.001 HIS A 287 PHE 0.011 0.001 PHE A 339 TYR 0.012 0.001 TYR R 85 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.072 Fit side-chains REVERT: A 221 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 258 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8588 (mt) REVERT: B 19 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7654 (ttp80) REVERT: B 156 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: G 22 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7528 (mt-10) outliers start: 32 outliers final: 24 residues processed: 174 average time/residue: 0.1947 time to fit residues: 47.9600 Evaluate side-chains 169 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 55 optimal weight: 0.0770 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS H 183 GLN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9074 Z= 0.156 Angle : 0.566 7.283 12348 Z= 0.288 Chirality : 0.042 0.181 1424 Planarity : 0.004 0.058 1540 Dihedral : 7.212 85.744 1402 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.09 % Allowed : 22.12 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.73 (0.25), residues: 1134 helix: 1.24 (0.26), residues: 394 sheet: -0.96 (0.32), residues: 245 loop : -1.66 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 287 PHE 0.011 0.001 PHE A 255 TYR 0.014 0.001 TYR G 40 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 0.951 Fit side-chains REVERT: A 221 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 258 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 271 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8164 (tt) REVERT: H 227 TYR cc_start: 0.7813 (m-10) cc_final: 0.7446 (m-80) REVERT: B 19 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7661 (ttp80) REVERT: B 127 LYS cc_start: 0.8856 (mttm) cc_final: 0.8649 (mmtt) REVERT: G 22 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7609 (mt-10) outliers start: 37 outliers final: 25 residues processed: 191 average time/residue: 0.1974 time to fit residues: 53.2683 Evaluate side-chains 170 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS H 183 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9074 Z= 0.156 Angle : 0.566 7.283 12348 Z= 0.288 Chirality : 0.042 0.181 1424 Planarity : 0.004 0.058 1540 Dihedral : 7.212 85.744 1402 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.21 % Allowed : 24.23 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.73 (0.25), residues: 1134 helix: 1.24 (0.26), residues: 394 sheet: -0.96 (0.32), residues: 245 loop : -1.66 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 287 PHE 0.011 0.001 PHE A 255 TYR 0.014 0.001 TYR G 40 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.031 Fit side-chains REVERT: A 221 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 258 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 271 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8164 (tt) REVERT: H 227 TYR cc_start: 0.7810 (m-10) cc_final: 0.7446 (m-80) REVERT: B 19 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.7661 (ttp80) REVERT: B 127 LYS cc_start: 0.8851 (mttm) cc_final: 0.8649 (mmtt) REVERT: G 22 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7609 (mt-10) outliers start: 29 outliers final: 25 residues processed: 164 average time/residue: 0.1957 time to fit residues: 45.4880 Evaluate side-chains 177 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 0.0570 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.0470 chunk 43 optimal weight: 0.0770 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS H 183 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9074 Z= 0.156 Angle : 0.566 7.283 12348 Z= 0.288 Chirality : 0.042 0.181 1424 Planarity : 0.004 0.058 1540 Dihedral : 7.212 85.744 1402 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.21 % Allowed : 24.12 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.73 (0.25), residues: 1134 helix: 1.24 (0.26), residues: 394 sheet: -0.96 (0.32), residues: 245 loop : -1.66 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 287 PHE 0.011 0.001 PHE A 255 TYR 0.014 0.001 TYR G 40 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.018 Fit side-chains REVERT: A 221 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 258 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8530 (mt) REVERT: A 271 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8164 (tt) REVERT: H 227 TYR cc_start: 0.7810 (m-10) cc_final: 0.7446 (m-80) REVERT: B 19 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.7661 (ttp80) REVERT: B 127 LYS cc_start: 0.8852 (mttm) cc_final: 0.8649 (mmtt) REVERT: G 22 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7610 (mt-10) outliers start: 29 outliers final: 25 residues processed: 171 average time/residue: 0.1956 time to fit residues: 47.4214 Evaluate side-chains 177 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS H 183 GLN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9074 Z= 0.180 Angle : 0.596 6.949 12348 Z= 0.304 Chirality : 0.043 0.286 1424 Planarity : 0.004 0.057 1540 Dihedral : 7.202 88.634 1402 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.65 % Allowed : 24.00 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.25), residues: 1134 helix: 1.35 (0.26), residues: 394 sheet: -0.86 (0.32), residues: 242 loop : -1.52 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.005 0.001 HIS H 167 PHE 0.011 0.001 PHE A 339 TYR 0.010 0.001 TYR A 235 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.7933 (ttp) cc_final: 0.7707 (ttm) REVERT: A 221 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 258 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8548 (mt) REVERT: A 271 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8140 (tt) REVERT: A 294 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7106 (pm20) REVERT: H 227 TYR cc_start: 0.7838 (m-10) cc_final: 0.7468 (m-80) REVERT: B 19 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.7674 (ttp80) REVERT: G 22 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7634 (mt-10) outliers start: 33 outliers final: 23 residues processed: 179 average time/residue: 0.1894 time to fit residues: 47.4649 Evaluate side-chains 176 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS H 183 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9074 Z= 0.270 Angle : 0.626 7.290 12348 Z= 0.320 Chirality : 0.044 0.282 1424 Planarity : 0.004 0.056 1540 Dihedral : 7.193 89.767 1402 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.65 % Allowed : 24.00 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.25), residues: 1134 helix: 1.36 (0.26), residues: 393 sheet: -0.84 (0.33), residues: 242 loop : -1.54 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 82 HIS 0.014 0.001 HIS A 287 PHE 0.012 0.001 PHE A 341 TYR 0.015 0.001 TYR G 40 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 0.967 Fit side-chains REVERT: A 203 MET cc_start: 0.7992 (ttp) cc_final: 0.7751 (ttm) REVERT: A 221 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7361 (tm-30) REVERT: A 258 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 271 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8127 (tt) REVERT: A 294 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7124 (pm20) REVERT: R 217 ASN cc_start: 0.7966 (t0) cc_final: 0.7688 (t0) REVERT: H 227 TYR cc_start: 0.7917 (m-10) cc_final: 0.7530 (m-80) REVERT: B 19 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.7672 (ttp80) REVERT: G 22 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7667 (mt-10) outliers start: 33 outliers final: 27 residues processed: 172 average time/residue: 0.1852 time to fit residues: 45.3758 Evaluate side-chains 170 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0050 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS H 183 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9074 Z= 0.154 Angle : 0.592 7.515 12348 Z= 0.300 Chirality : 0.042 0.242 1424 Planarity : 0.004 0.058 1540 Dihedral : 7.027 86.906 1402 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.43 % Allowed : 24.45 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.38 (0.25), residues: 1134 helix: 1.51 (0.27), residues: 393 sheet: -0.75 (0.32), residues: 242 loop : -1.43 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS H 167 PHE 0.011 0.001 PHE A 255 TYR 0.011 0.001 TYR A 285 ARG 0.004 0.000 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.016 Fit side-chains REVERT: A 203 MET cc_start: 0.7933 (ttp) cc_final: 0.7701 (ttm) REVERT: A 221 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 258 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8543 (mt) REVERT: A 271 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8122 (tt) REVERT: R 217 ASN cc_start: 0.7937 (t0) cc_final: 0.7653 (t0) REVERT: R 372 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7915 (tp) REVERT: R 392 LYS cc_start: 0.7248 (mmmt) cc_final: 0.7036 (mmmt) REVERT: H 227 TYR cc_start: 0.7832 (m-10) cc_final: 0.7465 (m-80) REVERT: B 19 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.7673 (ttp80) REVERT: G 22 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7609 (mt-10) outliers start: 31 outliers final: 23 residues processed: 171 average time/residue: 0.2008 time to fit residues: 48.0326 Evaluate side-chains 173 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 372 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS H 183 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.128936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102687 restraints weight = 13671.337| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.31 r_work: 0.3078 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9074 Z= 0.319 Angle : 0.660 8.257 12348 Z= 0.337 Chirality : 0.046 0.250 1424 Planarity : 0.004 0.055 1540 Dihedral : 7.140 83.470 1402 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.21 % Allowed : 24.45 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.51 (0.25), residues: 1134 helix: 1.32 (0.26), residues: 395 sheet: -0.80 (0.33), residues: 242 loop : -1.45 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.007 0.001 HIS A 287 PHE 0.016 0.002 PHE A 341 TYR 0.014 0.002 TYR G 40 ARG 0.004 0.000 ARG H 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.46 seconds wall clock time: 41 minutes 1.95 seconds (2461.95 seconds total)