Starting phenix.real_space_refine on Sat Aug 3 20:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzf_38794/08_2024/8xzf_38794.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzf_38794/08_2024/8xzf_38794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzf_38794/08_2024/8xzf_38794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzf_38794/08_2024/8xzf_38794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzf_38794/08_2024/8xzf_38794.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzf_38794/08_2024/8xzf_38794.cif" } resolution = 3.0 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= 0.001 sd= 0.005 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 73 5.16 5 C 5774 2.51 5 N 1534 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 168": "NH1" <-> "NH2" Residue "R TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 284": "OD1" <-> "OD2" Residue "R TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 62": "OD1" <-> "OD2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 189": "OD1" <-> "OD2" Residue "S PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 4": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9062 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2404 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1736 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2595 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 2, 'TRANS': 7} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2} Time building chain proxies: 5.24, per 1000 atoms: 0.58 Number of scatterers: 9062 At special positions: 0 Unit cell: (98.58, 132.06, 116.25, 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 73 16.00 O 1681 8.00 N 1534 7.00 C 5774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.03 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.02 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " 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: 3.55 Conformation dependent library (CDL) restraints added in 1.6 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB MED L 11 " Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 37.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'R' and resid 26 through 55 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.063A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 132 Processing helix chain 'R' and resid 135 through 139 removed outlier: 3.536A pdb=" N ALA R 138 " --> pdb=" O VAL R 135 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG R 139 " --> pdb=" O ALA R 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 135 through 139' Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 167 Processing helix chain 'R' and resid 193 through 211 removed outlier: 3.839A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 232 Processing helix chain 'R' and resid 236 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 281 through 305 Proline residue: R 292 - end of helix removed outlier: 3.561A pdb=" N ASN R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS R 303 " --> pdb=" O TYR R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.593A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.835A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 4.181A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.810A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.807A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.519A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.769A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.587A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.440A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.742A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.836A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.679A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.566A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.476A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.610A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.926A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.939A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.492A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1281 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: 2.55 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2896 1.34 - 1.46: 2283 1.46 - 1.58: 3976 1.58 - 1.70: 0 1.70 - 1.83: 105 Bond restraints: 9260 Sorted by residual: bond pdb=" N MET B 325 " pdb=" CA MET B 325 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.99e+00 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.57e+00 bond pdb=" N TRP R 279 " pdb=" CA TRP R 279 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.17e-02 7.31e+03 8.00e+00 bond pdb=" N ILE A 253 " pdb=" CA ILE A 253 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.79e+00 bond pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.77e+00 ... (remaining 9255 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.95: 158 105.95 - 113.02: 5018 113.02 - 120.09: 3267 120.09 - 127.17: 4006 127.17 - 134.24: 101 Bond angle restraints: 12550 Sorted by residual: angle pdb=" O ILE B 37 " pdb=" C ILE B 37 " pdb=" N ASP B 38 " ideal model delta sigma weight residual 121.83 127.09 -5.26 1.03e+00 9.43e-01 2.61e+01 angle pdb=" CA GLY B 41 " pdb=" C GLY B 41 " pdb=" O GLY B 41 " ideal model delta sigma weight residual 122.13 117.72 4.41 8.90e-01 1.26e+00 2.45e+01 angle pdb=" C ASN R 175 " pdb=" N THR R 176 " pdb=" CA THR R 176 " ideal model delta sigma weight residual 121.98 114.54 7.44 1.53e+00 4.27e-01 2.36e+01 angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 119.76 124.60 -4.84 1.03e+00 9.43e-01 2.21e+01 angle pdb=" N MET B 325 " pdb=" CA MET B 325 " pdb=" C MET B 325 " ideal model delta sigma weight residual 111.14 115.52 -4.38 1.08e+00 8.57e-01 1.65e+01 ... (remaining 12545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5012 17.86 - 35.71: 392 35.71 - 53.57: 48 53.57 - 71.43: 9 71.43 - 89.29: 9 Dihedral angle restraints: 5470 sinusoidal: 2104 harmonic: 3366 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 281 " pdb=" CB CYS R 281 " ideal model delta sinusoidal sigma weight residual -86.00 -5.21 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 149.27 -56.27 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" C ASP B 38 " pdb=" N ASP B 38 " pdb=" CA ASP B 38 " pdb=" CB ASP B 38 " ideal model delta harmonic sigma weight residual -122.60 -134.89 12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 5467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1265 0.078 - 0.157: 150 0.157 - 0.235: 4 0.235 - 0.314: 0 0.314 - 0.392: 1 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ASP B 38 " pdb=" N ASP B 38 " pdb=" C ASP B 38 " pdb=" CB ASP B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA LEU R 276 " pdb=" N LEU R 276 " pdb=" C LEU R 276 " pdb=" CB LEU R 276 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA LEU R 277 " pdb=" N LEU R 277 " pdb=" C LEU R 277 " pdb=" CB LEU R 277 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 1417 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 175 " -0.014 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C ASN R 175 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN R 175 " -0.016 2.00e-02 2.50e+03 pdb=" N THR R 176 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 36 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C ASN B 36 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN B 36 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE B 37 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER S 71 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.04e+00 pdb=" C SER S 71 " 0.039 2.00e-02 2.50e+03 pdb=" O SER S 71 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG S 72 " -0.013 2.00e-02 2.50e+03 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1461 2.76 - 3.47: 12417 3.47 - 4.19: 23134 4.19 - 4.90: 41718 Nonbonded interactions: 78731 Sorted by model distance: nonbonded pdb=" C PRO L 10 " pdb=" N MED L 11 " model vdw 1.326 3.350 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.091 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.093 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.144 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.231 3.040 ... (remaining 78726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.007 0.065 9260 Z= 0.450 Angle : 0.717 8.320 12550 Z= 0.426 Chirality : 0.049 0.392 1420 Planarity : 0.004 0.052 1581 Dihedral : 12.983 89.287 3285 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 0.51 % Allowed : 4.60 % Favored : 94.89 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.86 % 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: -2.36 (0.22), residues: 1139 helix: -1.03 (0.22), residues: 407 sheet: -1.41 (0.28), residues: 297 loop : -2.01 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 63 HIS 0.003 0.001 HIS B 91 PHE 0.022 0.002 PHE B 151 TYR 0.017 0.002 TYR S 103 ARG 0.006 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7409 (mp0) cc_final: 0.7040 (pm20) REVERT: B 124 TYR cc_start: 0.8682 (m-80) cc_final: 0.8464 (m-80) REVERT: B 130 GLU cc_start: 0.7823 (mp0) cc_final: 0.7470 (mp0) REVERT: B 256 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7426 (mtm-85) REVERT: S 83 MET cc_start: 0.8734 (mtm) cc_final: 0.8488 (mtp) outliers start: 5 outliers final: 0 residues processed: 169 average time/residue: 1.4125 time to fit residues: 252.0935 Evaluate side-chains 134 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 ASN R 112 ASN A 213 HIS B 91 HIS B 259 GLN S 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9260 Z= 0.197 Angle : 0.585 8.037 12550 Z= 0.308 Chirality : 0.042 0.147 1420 Planarity : 0.004 0.045 1581 Dihedral : 4.723 22.723 1262 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 1.74 % Allowed : 11.95 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.92 (0.24), residues: 1139 helix: 0.50 (0.25), residues: 408 sheet: -0.80 (0.29), residues: 285 loop : -1.42 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.005 0.001 HIS R 278 PHE 0.012 0.001 PHE L 14 TYR 0.019 0.001 TYR R 299 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 198 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6329 (pm20) REVERT: A 29 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7760 (tppt) REVERT: A 247 MET cc_start: 0.8378 (mtp) cc_final: 0.8079 (mtt) REVERT: A 289 GLU cc_start: 0.7398 (mp0) cc_final: 0.7018 (pm20) REVERT: A 313 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7589 (mtt90) REVERT: B 96 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7748 (mpt-90) REVERT: B 124 TYR cc_start: 0.8586 (m-80) cc_final: 0.8314 (m-80) REVERT: B 130 GLU cc_start: 0.7808 (mp0) cc_final: 0.7494 (mp0) REVERT: B 135 VAL cc_start: 0.8836 (t) cc_final: 0.8635 (p) REVERT: G 52 THR cc_start: 0.8317 (m) cc_final: 0.8039 (p) outliers start: 17 outliers final: 5 residues processed: 144 average time/residue: 1.5334 time to fit residues: 232.9480 Evaluate side-chains 127 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 232 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 102 optimal weight: 0.0670 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9260 Z= 0.172 Angle : 0.543 7.830 12550 Z= 0.285 Chirality : 0.041 0.143 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.335 20.439 1262 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.53 % Allowed : 14.10 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.20 (0.25), residues: 1139 helix: 1.25 (0.26), residues: 404 sheet: -0.42 (0.29), residues: 285 loop : -1.17 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 278 PHE 0.011 0.001 PHE B 151 TYR 0.014 0.001 TYR S 178 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8305 (mtp) cc_final: 0.8005 (mtt) REVERT: A 289 GLU cc_start: 0.7271 (mp0) cc_final: 0.6822 (pm20) REVERT: A 313 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7564 (mtt90) REVERT: B 124 TYR cc_start: 0.8541 (m-80) cc_final: 0.8242 (m-80) REVERT: B 130 GLU cc_start: 0.7808 (mp0) cc_final: 0.7420 (mp0) REVERT: B 138 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: G 21 MET cc_start: 0.6626 (ttt) cc_final: 0.6251 (mpm) REVERT: S 182 ASN cc_start: 0.8727 (m110) cc_final: 0.8418 (m110) REVERT: S 208 GLU cc_start: 0.7466 (mp0) cc_final: 0.7236 (mp0) REVERT: S 233 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7802 (mp) outliers start: 15 outliers final: 3 residues processed: 145 average time/residue: 1.4634 time to fit residues: 224.6534 Evaluate side-chains 128 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9260 Z= 0.211 Angle : 0.552 8.356 12550 Z= 0.289 Chirality : 0.042 0.171 1420 Planarity : 0.004 0.053 1581 Dihedral : 4.395 24.774 1262 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.35 % Allowed : 15.73 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.02 (0.25), residues: 1139 helix: 1.44 (0.26), residues: 404 sheet: -0.33 (0.29), residues: 286 loop : -1.02 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 278 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR S 178 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 162 MET cc_start: 0.7850 (tpt) cc_final: 0.7561 (mmt) REVERT: R 217 MET cc_start: 0.7546 (mtp) cc_final: 0.7301 (mtp) REVERT: R 262 MET cc_start: 0.7093 (tpt) cc_final: 0.6871 (tpt) REVERT: R 271 TYR cc_start: 0.7429 (t80) cc_final: 0.6734 (t80) REVERT: A 29 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7779 (tppt) REVERT: A 275 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7084 (pt0) REVERT: A 289 GLU cc_start: 0.7272 (mp0) cc_final: 0.6775 (pm20) REVERT: A 313 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7246 (ptp-110) REVERT: B 124 TYR cc_start: 0.8581 (m-80) cc_final: 0.8254 (m-80) REVERT: B 130 GLU cc_start: 0.7867 (mp0) cc_final: 0.7537 (mp0) REVERT: S 182 ASN cc_start: 0.8774 (m110) cc_final: 0.8402 (m110) outliers start: 23 outliers final: 8 residues processed: 141 average time/residue: 1.2777 time to fit residues: 191.9965 Evaluate side-chains 134 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 197 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9260 Z= 0.233 Angle : 0.550 8.004 12550 Z= 0.289 Chirality : 0.042 0.161 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.448 28.529 1262 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.06 % Allowed : 15.83 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.11 (0.25), residues: 1139 helix: 1.55 (0.26), residues: 403 sheet: -0.23 (0.30), residues: 277 loop : -1.02 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 278 PHE 0.012 0.001 PHE B 151 TYR 0.023 0.001 TYR R 271 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: R 101 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5429 (m-10) REVERT: R 162 MET cc_start: 0.7901 (tpt) cc_final: 0.7655 (mmt) REVERT: R 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6470 (tpt) REVERT: R 198 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6417 (pm20) REVERT: R 217 MET cc_start: 0.7557 (mtp) cc_final: 0.7292 (mtp) REVERT: R 235 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: A 29 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7832 (tppt) REVERT: A 247 MET cc_start: 0.8256 (mtp) cc_final: 0.7820 (mtt) REVERT: A 275 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7013 (pt0) REVERT: A 289 GLU cc_start: 0.7274 (mp0) cc_final: 0.6748 (pm20) REVERT: B 124 TYR cc_start: 0.8544 (m-80) cc_final: 0.8235 (m-80) REVERT: B 130 GLU cc_start: 0.7825 (mp0) cc_final: 0.7476 (mp0) REVERT: S 208 GLU cc_start: 0.7341 (mp0) cc_final: 0.7042 (mp0) outliers start: 30 outliers final: 11 residues processed: 150 average time/residue: 1.3514 time to fit residues: 215.4349 Evaluate side-chains 146 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 197 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9260 Z= 0.417 Angle : 0.634 7.830 12550 Z= 0.333 Chirality : 0.046 0.155 1420 Planarity : 0.005 0.051 1581 Dihedral : 4.910 33.823 1262 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.27 % Allowed : 16.75 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.10 (0.25), residues: 1139 helix: 1.24 (0.26), residues: 402 sheet: -0.19 (0.30), residues: 279 loop : -1.11 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 63 HIS 0.003 0.001 HIS A 244 PHE 0.016 0.002 PHE B 151 TYR 0.020 0.002 TYR R 185 ARG 0.008 0.001 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.092 Fit side-chains REVERT: R 101 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5569 (m-10) REVERT: R 162 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7621 (mmt) REVERT: R 165 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6525 (tpt) REVERT: R 198 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6153 (pm20) REVERT: R 235 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6817 (mm-30) REVERT: R 271 TYR cc_start: 0.7126 (t80) cc_final: 0.6625 (t80) REVERT: A 29 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7782 (tppt) REVERT: A 247 MET cc_start: 0.8309 (mtp) cc_final: 0.7865 (mtt) REVERT: A 275 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7116 (pt0) REVERT: A 289 GLU cc_start: 0.7313 (mp0) cc_final: 0.6745 (pm20) REVERT: A 313 ARG cc_start: 0.7939 (mpt90) cc_final: 0.7351 (ptp-110) REVERT: B 124 TYR cc_start: 0.8636 (m-80) cc_final: 0.8282 (m-80) REVERT: B 130 GLU cc_start: 0.7836 (mp0) cc_final: 0.7510 (mp0) outliers start: 32 outliers final: 12 residues processed: 154 average time/residue: 1.3312 time to fit residues: 218.1116 Evaluate side-chains 150 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9260 Z= 0.204 Angle : 0.544 8.630 12550 Z= 0.284 Chirality : 0.041 0.158 1420 Planarity : 0.004 0.049 1581 Dihedral : 4.548 35.041 1262 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.27 % Allowed : 16.85 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.13 (0.25), residues: 1139 helix: 1.54 (0.26), residues: 403 sheet: -0.16 (0.30), residues: 278 loop : -1.04 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 278 PHE 0.010 0.001 PHE B 151 TYR 0.017 0.001 TYR R 271 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.030 Fit side-chains REVERT: R 101 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5435 (m-10) REVERT: R 162 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7595 (mmt) REVERT: R 165 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6497 (tpt) REVERT: R 198 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: R 271 TYR cc_start: 0.7100 (t80) cc_final: 0.6609 (t80) REVERT: A 29 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7793 (tppt) REVERT: A 275 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7002 (pt0) REVERT: A 289 GLU cc_start: 0.7290 (mp0) cc_final: 0.6734 (pm20) REVERT: A 313 ARG cc_start: 0.7872 (mpt90) cc_final: 0.7514 (mmt-90) REVERT: B 124 TYR cc_start: 0.8542 (m-80) cc_final: 0.8220 (m-80) REVERT: B 130 GLU cc_start: 0.7838 (mp0) cc_final: 0.7482 (mp0) outliers start: 32 outliers final: 16 residues processed: 153 average time/residue: 1.3348 time to fit residues: 216.8483 Evaluate side-chains 151 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 137 ASN Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 113 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN G 59 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9260 Z= 0.184 Angle : 0.542 8.962 12550 Z= 0.281 Chirality : 0.041 0.172 1420 Planarity : 0.004 0.050 1581 Dihedral : 4.424 36.581 1262 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.06 % Allowed : 17.26 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.27 (0.25), residues: 1139 helix: 1.70 (0.26), residues: 403 sheet: -0.10 (0.31), residues: 270 loop : -0.97 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS R 231 PHE 0.010 0.001 PHE B 151 TYR 0.017 0.001 TYR R 271 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.038 Fit side-chains REVERT: R 101 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5425 (m-10) REVERT: R 162 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7601 (mmt) REVERT: R 165 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6478 (tpt) REVERT: R 198 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.6023 (pm20) REVERT: R 271 TYR cc_start: 0.6991 (t80) cc_final: 0.6508 (t80) REVERT: A 29 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7840 (tppt) REVERT: A 246 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 247 MET cc_start: 0.8256 (mtp) cc_final: 0.7824 (mtt) REVERT: A 275 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7064 (pt0) REVERT: A 313 ARG cc_start: 0.7857 (mpt90) cc_final: 0.7161 (ptp-110) REVERT: B 124 TYR cc_start: 0.8522 (m-80) cc_final: 0.8199 (m-80) REVERT: B 130 GLU cc_start: 0.7856 (mp0) cc_final: 0.7503 (mp0) REVERT: B 214 ARG cc_start: 0.7404 (mmp80) cc_final: 0.7170 (mmp80) REVERT: B 237 ASN cc_start: 0.8299 (p0) cc_final: 0.8064 (p0) REVERT: S 171 GLN cc_start: 0.7810 (mt0) cc_final: 0.7541 (mt0) outliers start: 30 outliers final: 14 residues processed: 151 average time/residue: 1.3396 time to fit residues: 215.7972 Evaluate side-chains 151 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 137 ASN Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 197 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9260 Z= 0.291 Angle : 0.591 9.521 12550 Z= 0.304 Chirality : 0.043 0.166 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.632 35.342 1262 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 3.06 % Allowed : 17.47 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1139 helix: 1.54 (0.26), residues: 403 sheet: -0.15 (0.31), residues: 270 loop : -1.01 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE B 151 TYR 0.028 0.002 TYR R 185 ARG 0.005 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.190 Fit side-chains REVERT: R 55 ARG cc_start: 0.5859 (tpt-90) cc_final: 0.5541 (tpp80) REVERT: R 101 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5438 (m-10) REVERT: R 162 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7580 (mmt) REVERT: R 165 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6519 (tpt) REVERT: R 198 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.6021 (pm20) REVERT: R 235 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6871 (mm-30) REVERT: R 271 TYR cc_start: 0.7013 (t80) cc_final: 0.6525 (t80) REVERT: A 29 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7833 (tppt) REVERT: A 247 MET cc_start: 0.8269 (mtp) cc_final: 0.7833 (mtt) REVERT: A 275 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7066 (pt0) REVERT: A 313 ARG cc_start: 0.7894 (mpt90) cc_final: 0.7217 (ptp-110) REVERT: B 124 TYR cc_start: 0.8568 (m-80) cc_final: 0.8224 (m-80) REVERT: B 130 GLU cc_start: 0.7859 (mp0) cc_final: 0.7546 (mp0) REVERT: S 171 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7608 (mt0) outliers start: 30 outliers final: 14 residues processed: 150 average time/residue: 1.3138 time to fit residues: 209.2942 Evaluate side-chains 149 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 137 ASN Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 171 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN G 59 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9260 Z= 0.196 Angle : 0.556 9.720 12550 Z= 0.286 Chirality : 0.042 0.166 1420 Planarity : 0.004 0.050 1581 Dihedral : 4.426 36.010 1262 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 2.55 % Allowed : 17.67 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.28 (0.25), residues: 1139 helix: 1.69 (0.26), residues: 403 sheet: -0.06 (0.31), residues: 270 loop : -0.99 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 231 PHE 0.010 0.001 PHE B 151 TYR 0.023 0.001 TYR R 185 ARG 0.007 0.000 ARG S 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.040 Fit side-chains REVERT: R 55 ARG cc_start: 0.5876 (tpt-90) cc_final: 0.5597 (tpp80) REVERT: R 101 PHE cc_start: 0.6016 (OUTLIER) cc_final: 0.5435 (m-10) REVERT: R 162 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7589 (mmt) REVERT: R 165 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6512 (tpt) REVERT: R 198 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5741 (pm20) REVERT: R 235 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6781 (mm-30) REVERT: R 271 TYR cc_start: 0.6957 (t80) cc_final: 0.6462 (t80) REVERT: A 29 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7851 (tppt) REVERT: A 246 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.7852 (p) REVERT: A 247 MET cc_start: 0.8275 (mtp) cc_final: 0.7808 (mtt) REVERT: A 275 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7028 (pt0) REVERT: A 313 ARG cc_start: 0.7848 (mpt90) cc_final: 0.7140 (ptp-110) REVERT: B 124 TYR cc_start: 0.8540 (m-80) cc_final: 0.8200 (m-80) REVERT: B 130 GLU cc_start: 0.7863 (mp0) cc_final: 0.7506 (mp0) REVERT: B 201 SER cc_start: 0.8474 (m) cc_final: 0.8254 (p) REVERT: B 237 ASN cc_start: 0.8317 (p0) cc_final: 0.8080 (p0) REVERT: G 21 MET cc_start: 0.6520 (ptm) cc_final: 0.6061 (mpm) REVERT: S 171 GLN cc_start: 0.7777 (mt0) cc_final: 0.7543 (mt0) outliers start: 25 outliers final: 13 residues processed: 148 average time/residue: 1.3035 time to fit residues: 204.8962 Evaluate side-chains 148 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 137 ASN Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.087361 restraints weight = 14484.260| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.79 r_work: 0.3131 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9260 Z= 0.252 Angle : 0.576 9.339 12550 Z= 0.298 Chirality : 0.043 0.165 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.520 35.001 1262 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.66 % Allowed : 17.77 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.21 (0.25), residues: 1139 helix: 1.61 (0.26), residues: 403 sheet: -0.09 (0.31), residues: 270 loop : -1.01 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.025 0.002 TYR R 185 ARG 0.005 0.001 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3919.74 seconds wall clock time: 69 minutes 6.79 seconds (4146.79 seconds total)