Starting phenix.real_space_refine on Tue Mar 19 18:41:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/03_2024/7e51_30989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/03_2024/7e51_30989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/03_2024/7e51_30989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/03_2024/7e51_30989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/03_2024/7e51_30989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/03_2024/7e51_30989_updated.pdb" } resolution = 3.23 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= 0.006 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 16 5.21 5 S 56 5.16 5 C 15608 2.51 5 N 4320 2.21 5 O 5024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 404": "NH1" <-> "NH2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 223": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E ARG 223": "NH1" <-> "NH2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E ARG 261": "NH1" <-> "NH2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E ARG 358": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F ARG 223": "NH1" <-> "NH2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "G ARG 10": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G GLU 195": "OE1" <-> "OE2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "G ARG 261": "NH1" <-> "NH2" Residue "G GLU 322": "OE1" <-> "OE2" Residue "G GLU 344": "OE1" <-> "OE2" Residue "G ARG 358": "NH1" <-> "NH2" Residue "G ARG 404": "NH1" <-> "NH2" Residue "H ARG 10": "NH1" <-> "NH2" Residue "H ARG 104": "NH1" <-> "NH2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H ARG 223": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 261": "NH1" <-> "NH2" Residue "H GLU 318": "OE1" <-> "OE2" Residue "H GLU 321": "OE1" <-> "OE2" Residue "H GLU 344": "OE1" <-> "OE2" Residue "H ARG 358": "NH1" <-> "NH2" Residue "H ARG 404": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25032 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "B" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "D" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "E" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "F" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "G" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "H" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.56, per 1000 atoms: 0.50 Number of scatterers: 25032 At special positions: 0 Unit cell: (159.43, 159.43, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 8 15.00 Mg 16 11.99 O 5024 8.00 N 4320 7.00 C 15608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.52 Conformation dependent library (CDL) restraints added in 4.5 seconds 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 26 sheets defined 39.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.521A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 78' Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 109 through 123 removed outlier: 4.005A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.537A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 134 " --> pdb=" O PHE A 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 134' Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.755A pdb=" N SER A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.613A pdb=" N GLY A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.789A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.772A pdb=" N GLU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 396 through 412 removed outlier: 6.589A pdb=" N ASP A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ALA A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 86 through 97 Processing helix chain 'B' and resid 109 through 121 removed outlier: 3.952A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.670A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 134' Processing helix chain 'B' and resid 174 through 194 Processing helix chain 'B' and resid 214 through 228 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 317 through 325 removed outlier: 3.698A pdb=" N GLU B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 396 through 412 removed outlier: 6.405A pdb=" N ASP B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 60 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.555A pdb=" N VAL C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 78' Processing helix chain 'C' and resid 86 through 97 removed outlier: 3.792A pdb=" N GLN C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 174 through 195 removed outlier: 3.606A pdb=" N SER C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 228 Processing helix chain 'C' and resid 244 through 247 Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.663A pdb=" N ALA C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 317 through 325 removed outlier: 3.886A pdb=" N GLU C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 396 through 412 removed outlier: 6.412A pdb=" N ASP C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 60 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 86 through 97 Processing helix chain 'D' and resid 107 through 124 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 174 through 195 Processing helix chain 'D' and resid 214 through 228 Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 291 through 301 Processing helix chain 'D' and resid 317 through 325 removed outlier: 3.747A pdb=" N GLU D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.683A pdb=" N GLY D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'D' and resid 396 through 412 removed outlier: 6.347A pdb=" N ASP D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 60 Processing helix chain 'E' and resid 64 through 72 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 107 through 124 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 174 through 194 Processing helix chain 'E' and resid 214 through 228 Processing helix chain 'E' and resid 244 through 247 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 317 through 325 removed outlier: 3.703A pdb=" N GLU E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 342 through 353 Processing helix chain 'E' and resid 372 through 379 Processing helix chain 'E' and resid 396 through 412 removed outlier: 6.424A pdb=" N ASP E 411 " --> pdb=" O GLU E 407 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 60 Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 86 through 97 Processing helix chain 'F' and resid 107 through 124 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 174 through 195 Processing helix chain 'F' and resid 214 through 228 Processing helix chain 'F' and resid 244 through 247 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 291 through 301 Processing helix chain 'F' and resid 317 through 325 removed outlier: 3.751A pdb=" N GLU F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.664A pdb=" N GLY F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 379 Processing helix chain 'F' and resid 396 through 412 removed outlier: 6.361A pdb=" N ASP F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 60 Processing helix chain 'G' and resid 64 through 72 Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 86 through 97 Processing helix chain 'G' and resid 107 through 124 Processing helix chain 'G' and resid 129 through 134 Processing helix chain 'G' and resid 174 through 194 Processing helix chain 'G' and resid 214 through 228 Processing helix chain 'G' and resid 244 through 247 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 291 through 301 Processing helix chain 'G' and resid 317 through 325 removed outlier: 3.926A pdb=" N GLU G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'G' and resid 342 through 353 Processing helix chain 'G' and resid 372 through 379 Processing helix chain 'G' and resid 396 through 412 removed outlier: 6.361A pdb=" N ASP G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA G 412 " --> pdb=" O ALA G 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 60 Processing helix chain 'H' and resid 64 through 72 Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'H' and resid 107 through 124 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'H' and resid 174 through 194 Processing helix chain 'H' and resid 214 through 228 Processing helix chain 'H' and resid 244 through 247 Processing helix chain 'H' and resid 263 through 276 Processing helix chain 'H' and resid 291 through 301 Processing helix chain 'H' and resid 317 through 325 removed outlier: 3.744A pdb=" N GLU H 322 " --> pdb=" O GLU H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 338 No H-bonds generated for 'chain 'H' and resid 336 through 338' Processing helix chain 'H' and resid 342 through 353 Processing helix chain 'H' and resid 372 through 379 Processing helix chain 'H' and resid 396 through 412 removed outlier: 6.352A pdb=" N ASP H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA H 412 " --> pdb=" O ALA H 408 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.892A pdb=" N PHE A 164 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 167 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 240 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 282 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN A 306 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 254 through 256 Processing sheet with id= C, first strand: chain 'A' and resid 331 through 334 removed outlier: 6.769A pdb=" N ARG A 358 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 334 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET A 360 " --> pdb=" O VAL A 334 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 4 through 13 removed outlier: 6.758A pdb=" N ALA A 26 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 7 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU A 24 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA A 9 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 22 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 11 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR A 20 " --> pdb=" O GLU A 11 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 32 through 36 Processing sheet with id= F, first strand: chain 'B' and resid 145 through 150 removed outlier: 7.136A pdb=" N PHE B 164 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 167 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 240 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 282 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN B 306 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 331 through 334 removed outlier: 6.736A pdb=" N ARG B 358 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL B 334 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET B 360 " --> pdb=" O VAL B 334 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 384 through 386 removed outlier: 5.873A pdb=" N VAL C 143 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE C 164 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 167 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU C 240 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE C 282 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN C 306 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 254 through 256 Processing sheet with id= J, first strand: chain 'C' and resid 4 through 13 removed outlier: 6.714A pdb=" N ALA C 26 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL C 7 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU C 24 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA C 9 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU C 22 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU C 11 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR C 20 " --> pdb=" O GLU C 11 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'D' and resid 384 through 386 removed outlier: 5.910A pdb=" N VAL D 143 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 164 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 254 through 256 Processing sheet with id= N, first strand: chain 'D' and resid 281 through 283 removed outlier: 6.105A pdb=" N GLN D 306 " --> pdb=" O ILE D 282 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 32 through 36 Processing sheet with id= P, first strand: chain 'E' and resid 384 through 386 removed outlier: 5.933A pdb=" N VAL E 143 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE E 164 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 240 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE E 282 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN E 306 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 254 through 256 Processing sheet with id= R, first strand: chain 'F' and resid 32 through 36 Processing sheet with id= S, first strand: chain 'F' and resid 384 through 386 removed outlier: 5.966A pdb=" N VAL F 143 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE F 164 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU F 240 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE F 282 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN F 306 " --> pdb=" O ILE F 282 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 254 through 256 Processing sheet with id= U, first strand: chain 'G' and resid 32 through 36 Processing sheet with id= V, first strand: chain 'G' and resid 384 through 386 removed outlier: 5.896A pdb=" N VAL G 143 " --> pdb=" O ILE G 385 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE G 164 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU G 240 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE G 282 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN G 306 " --> pdb=" O ILE G 282 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 254 through 256 Processing sheet with id= X, first strand: chain 'H' and resid 32 through 36 Processing sheet with id= Y, first strand: chain 'H' and resid 384 through 386 removed outlier: 5.878A pdb=" N VAL H 143 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE H 164 " --> pdb=" O ILE H 148 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU H 240 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE H 282 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN H 306 " --> pdb=" O ILE H 282 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 254 through 256 removed outlier: 3.673A pdb=" N PHE H 256 " --> pdb=" O THR H 259 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2844 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: 7.40 Time building geometry restraints manager: 10.29 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: 8750 1.34 - 1.45: 2681 1.45 - 1.57: 13857 1.57 - 1.69: 8 1.69 - 1.81: 112 Bond restraints: 25408 Sorted by residual: bond pdb=" N GLU E 45 " pdb=" CA GLU E 45 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" N GLU E 47 " pdb=" CA GLU E 47 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.32e-02 5.74e+03 9.64e+00 bond pdb=" N THR G 43 " pdb=" CA THR G 43 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.83e+00 bond pdb=" N GLY D 40 " pdb=" CA GLY D 40 " ideal model delta sigma weight residual 1.448 1.476 -0.028 1.04e-02 9.25e+03 7.13e+00 bond pdb=" N THR H 43 " pdb=" CA THR H 43 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.92e+00 ... (remaining 25403 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.05: 492 105.05 - 112.29: 12765 112.29 - 119.52: 8556 119.52 - 126.76: 12486 126.76 - 134.00: 269 Bond angle restraints: 34568 Sorted by residual: angle pdb=" C2 PEP C 501 " pdb=" C1 PEP C 501 " pdb=" O2' PEP C 501 " ideal model delta sigma weight residual 113.54 120.43 -6.89 1.21e+00 6.82e-01 3.24e+01 angle pdb=" C2 PEP E 501 " pdb=" C1 PEP E 501 " pdb=" O2' PEP E 501 " ideal model delta sigma weight residual 113.54 120.42 -6.88 1.21e+00 6.82e-01 3.23e+01 angle pdb=" C2 PEP G 501 " pdb=" C1 PEP G 501 " pdb=" O2' PEP G 501 " ideal model delta sigma weight residual 113.54 120.37 -6.83 1.21e+00 6.82e-01 3.18e+01 angle pdb=" C2 PEP A 501 " pdb=" C1 PEP A 501 " pdb=" O2' PEP A 501 " ideal model delta sigma weight residual 113.54 120.31 -6.77 1.21e+00 6.82e-01 3.13e+01 angle pdb=" C1 PEP H 501 " pdb=" C2 PEP H 501 " pdb=" O2 PEP H 501 " ideal model delta sigma weight residual 111.24 120.19 -8.95 1.68e+00 3.56e-01 2.85e+01 ... (remaining 34563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13815 17.89 - 35.78: 1086 35.78 - 53.66: 132 53.66 - 71.55: 57 71.55 - 89.44: 38 Dihedral angle restraints: 15128 sinusoidal: 5680 harmonic: 9448 Sorted by residual: dihedral pdb=" CA ARG D 392 " pdb=" C ARG D 392 " pdb=" N SER D 393 " pdb=" CA SER D 393 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG F 392 " pdb=" C ARG F 392 " pdb=" N SER F 393 " pdb=" CA SER F 393 " ideal model delta harmonic sigma weight residual 180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG E 392 " pdb=" C ARG E 392 " pdb=" N SER E 393 " pdb=" CA SER E 393 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 15125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3065 0.051 - 0.103: 808 0.103 - 0.154: 111 0.154 - 0.206: 6 0.206 - 0.257: 2 Chirality restraints: 3992 Sorted by residual: chirality pdb=" CA GLU E 45 " pdb=" N GLU E 45 " pdb=" C GLU E 45 " pdb=" CB GLU E 45 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 328 " pdb=" N VAL B 328 " pdb=" C VAL B 328 " pdb=" CB VAL B 328 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB VAL A 305 " pdb=" CA VAL A 305 " pdb=" CG1 VAL A 305 " pdb=" CG2 VAL A 305 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3989 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 47 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C GLU E 47 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU E 47 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA E 48 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 328 " 0.011 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C VAL B 328 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL B 328 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 329 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 189 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C LYS B 189 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS B 189 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 190 " -0.014 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 387 2.62 - 3.19: 23143 3.19 - 3.76: 38829 3.76 - 4.33: 56012 4.33 - 4.90: 92200 Nonbonded interactions: 210571 Sorted by model distance: nonbonded pdb=" OE2 GLU B 283 " pdb="MG MG B 503 " model vdw 2.055 2.170 nonbonded pdb=" O2P PEP F 501 " pdb="MG MG F 502 " model vdw 2.069 2.170 nonbonded pdb=" OG SER H 42 " pdb="MG MG H 502 " model vdw 2.069 2.170 nonbonded pdb=" O2P PEP D 501 " pdb="MG MG D 502 " model vdw 2.074 2.170 nonbonded pdb=" O2P PEP E 501 " pdb="MG MG E 502 " model vdw 2.077 2.170 ... (remaining 210566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.710 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: 0.030 Extract box with map and model: 8.520 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 63.710 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25408 Z= 0.340 Angle : 0.689 8.951 34568 Z= 0.403 Chirality : 0.045 0.257 3992 Planarity : 0.004 0.052 4632 Dihedral : 14.036 89.439 9128 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.09 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.12), residues: 3368 helix: -1.02 (0.12), residues: 1368 sheet: -2.52 (0.20), residues: 536 loop : -2.92 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 294 HIS 0.007 0.001 HIS D 363 PHE 0.015 0.002 PHE B 247 TYR 0.009 0.001 TYR C 132 ARG 0.006 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.992 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7960 (pm20) cc_final: 0.7592 (pm20) REVERT: B 65 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8498 (ptmt) REVERT: C 47 GLU cc_start: 0.7782 (pm20) cc_final: 0.7572 (pm20) REVERT: C 264 ASP cc_start: 0.7355 (m-30) cc_final: 0.7126 (p0) REVERT: C 288 GLU cc_start: 0.7331 (pm20) cc_final: 0.6973 (pp20) REVERT: D 119 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7856 (mttp) REVERT: E 288 GLU cc_start: 0.7353 (pm20) cc_final: 0.7048 (pp20) REVERT: G 145 MET cc_start: 0.8833 (mmm) cc_final: 0.8608 (mmt) REVERT: G 321 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6883 (mm-30) REVERT: H 288 GLU cc_start: 0.7223 (pm20) cc_final: 0.6884 (pp20) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.4209 time to fit residues: 225.7268 Evaluate side-chains 216 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 0.0370 chunk 86 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 196 optimal weight: 0.0270 chunk 305 optimal weight: 0.8980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN F 6 GLN G 6 GLN H 6 GLN H 363 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25408 Z= 0.143 Angle : 0.479 5.855 34568 Z= 0.249 Chirality : 0.039 0.149 3992 Planarity : 0.003 0.032 4632 Dihedral : 4.917 55.408 3664 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.15 % Allowed : 7.56 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3368 helix: 0.62 (0.13), residues: 1384 sheet: -1.61 (0.25), residues: 384 loop : -2.39 (0.13), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 294 HIS 0.005 0.001 HIS D 363 PHE 0.020 0.002 PHE D 32 TYR 0.014 0.001 TYR C 357 ARG 0.002 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 262 time to evaluate : 2.850 Fit side-chains REVERT: A 47 GLU cc_start: 0.7985 (pm20) cc_final: 0.7577 (pm20) REVERT: B 65 LYS cc_start: 0.8543 (ptpt) cc_final: 0.8304 (ptmt) REVERT: C 264 ASP cc_start: 0.7381 (m-30) cc_final: 0.7115 (p0) REVERT: D 119 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7751 (mttp) REVERT: D 264 ASP cc_start: 0.7271 (m-30) cc_final: 0.6959 (p0) REVERT: F 119 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7687 (mttp) REVERT: F 264 ASP cc_start: 0.7386 (m-30) cc_final: 0.7127 (p0) REVERT: F 288 GLU cc_start: 0.7163 (pm20) cc_final: 0.6955 (pm20) REVERT: G 119 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7751 (mttp) REVERT: G 264 ASP cc_start: 0.7614 (m-30) cc_final: 0.7346 (p0) REVERT: G 322 GLU cc_start: 0.7354 (tt0) cc_final: 0.7015 (tp30) REVERT: G 351 LEU cc_start: 0.8622 (mp) cc_final: 0.8392 (mp) REVERT: H 264 ASP cc_start: 0.7120 (m-30) cc_final: 0.6899 (p0) REVERT: H 288 GLU cc_start: 0.7215 (pm20) cc_final: 0.6772 (pp20) outliers start: 29 outliers final: 10 residues processed: 288 average time/residue: 0.3584 time to fit residues: 163.1491 Evaluate side-chains 229 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 305 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 245 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25408 Z= 0.140 Angle : 0.450 4.849 34568 Z= 0.233 Chirality : 0.039 0.141 3992 Planarity : 0.003 0.027 4632 Dihedral : 4.531 50.218 3664 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 1.04 % Allowed : 10.11 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3368 helix: 1.41 (0.14), residues: 1384 sheet: -1.25 (0.25), residues: 384 loop : -2.14 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 294 HIS 0.004 0.000 HIS G 363 PHE 0.021 0.002 PHE G 32 TYR 0.016 0.001 TYR E 357 ARG 0.003 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 2.718 Fit side-chains revert: symmetry clash REVERT: C 47 GLU cc_start: 0.7943 (pm20) cc_final: 0.7620 (pt0) REVERT: C 288 GLU cc_start: 0.7204 (pm20) cc_final: 0.6933 (pm20) REVERT: C 351 LEU cc_start: 0.8523 (mp) cc_final: 0.8285 (mp) REVERT: D 119 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7731 (mttp) REVERT: D 264 ASP cc_start: 0.7282 (m-30) cc_final: 0.7059 (p0) REVERT: D 351 LEU cc_start: 0.8457 (mp) cc_final: 0.8217 (mp) REVERT: E 351 LEU cc_start: 0.8606 (mp) cc_final: 0.8377 (mp) REVERT: E 360 MET cc_start: 0.8407 (ttm) cc_final: 0.8205 (ttm) REVERT: F 119 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7664 (mttp) REVERT: F 256 PHE cc_start: 0.6530 (t80) cc_final: 0.6261 (t80) REVERT: F 264 ASP cc_start: 0.7391 (m-30) cc_final: 0.7167 (p0) REVERT: G 119 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7706 (mttp) REVERT: G 264 ASP cc_start: 0.7532 (m-30) cc_final: 0.7305 (p0) REVERT: G 322 GLU cc_start: 0.7458 (tt0) cc_final: 0.7094 (tp30) REVERT: G 351 LEU cc_start: 0.8586 (mp) cc_final: 0.8357 (mp) REVERT: H 264 ASP cc_start: 0.7120 (m-30) cc_final: 0.6898 (p0) REVERT: H 351 LEU cc_start: 0.8542 (mp) cc_final: 0.8304 (mp) outliers start: 26 outliers final: 19 residues processed: 256 average time/residue: 0.3673 time to fit residues: 148.8558 Evaluate side-chains 219 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9990 chunk 229 optimal weight: 0.2980 chunk 158 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 306 optimal weight: 8.9990 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25408 Z= 0.140 Angle : 0.433 5.050 34568 Z= 0.224 Chirality : 0.039 0.134 3992 Planarity : 0.003 0.026 4632 Dihedral : 4.272 43.461 3664 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.23 % Allowed : 11.11 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3368 helix: 1.82 (0.14), residues: 1384 sheet: -0.94 (0.26), residues: 384 loop : -1.98 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 294 HIS 0.004 0.000 HIS G 363 PHE 0.022 0.002 PHE C 32 TYR 0.016 0.001 TYR A 357 ARG 0.002 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 2.826 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7872 (pm20) cc_final: 0.7600 (pt0) REVERT: A 360 MET cc_start: 0.8430 (ttm) cc_final: 0.8215 (ttm) REVERT: B 194 LYS cc_start: 0.8814 (tmmt) cc_final: 0.8586 (ttpt) REVERT: C 47 GLU cc_start: 0.8004 (pm20) cc_final: 0.7587 (pt0) REVERT: C 360 MET cc_start: 0.8432 (ttm) cc_final: 0.8208 (ttm) REVERT: D 119 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7670 (mttp) REVERT: D 264 ASP cc_start: 0.7408 (m-30) cc_final: 0.7162 (p0) REVERT: E 351 LEU cc_start: 0.8575 (mp) cc_final: 0.8353 (mp) REVERT: E 360 MET cc_start: 0.8457 (ttm) cc_final: 0.8254 (ttm) REVERT: F 119 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7670 (mttp) REVERT: F 264 ASP cc_start: 0.7394 (m-30) cc_final: 0.7173 (p0) REVERT: F 360 MET cc_start: 0.8471 (ttm) cc_final: 0.8260 (ttm) REVERT: G 119 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7707 (mttp) REVERT: G 252 THR cc_start: 0.6834 (OUTLIER) cc_final: 0.6596 (t) REVERT: G 264 ASP cc_start: 0.7585 (m-30) cc_final: 0.7350 (p0) REVERT: G 322 GLU cc_start: 0.7423 (tt0) cc_final: 0.7028 (tp30) REVERT: G 351 LEU cc_start: 0.8587 (mp) cc_final: 0.8354 (mp) REVERT: H 264 ASP cc_start: 0.7109 (m-30) cc_final: 0.6871 (p0) REVERT: H 360 MET cc_start: 0.8441 (ttm) cc_final: 0.8240 (ttm) outliers start: 31 outliers final: 20 residues processed: 240 average time/residue: 0.3687 time to fit residues: 140.4202 Evaluate side-chains 220 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 chunk 224 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 25408 Z= 0.305 Angle : 0.498 4.725 34568 Z= 0.259 Chirality : 0.041 0.136 3992 Planarity : 0.004 0.030 4632 Dihedral : 4.401 37.988 3664 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 1.59 % Allowed : 12.50 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3368 helix: 1.93 (0.14), residues: 1328 sheet: -1.31 (0.22), residues: 536 loop : -1.81 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 294 HIS 0.008 0.001 HIS G 363 PHE 0.024 0.003 PHE H 32 TYR 0.015 0.002 TYR A 357 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 2.768 Fit side-chains revert: symmetry clash REVERT: A 326 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7016 (mtm180) REVERT: C 47 GLU cc_start: 0.8056 (pm20) cc_final: 0.7665 (pt0) REVERT: C 351 LEU cc_start: 0.8585 (mp) cc_final: 0.8344 (mp) REVERT: D 119 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7673 (mttp) REVERT: D 145 MET cc_start: 0.8764 (mmm) cc_final: 0.8273 (mmt) REVERT: D 264 ASP cc_start: 0.7208 (m-30) cc_final: 0.7003 (p0) REVERT: D 351 LEU cc_start: 0.8486 (mp) cc_final: 0.8245 (mp) REVERT: E 282 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8826 (pt) REVERT: F 119 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7664 (mttp) REVERT: F 145 MET cc_start: 0.8765 (mmm) cc_final: 0.8287 (mmm) REVERT: F 264 ASP cc_start: 0.7416 (m-30) cc_final: 0.7142 (p0) REVERT: G 119 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7687 (mttp) REVERT: G 264 ASP cc_start: 0.7483 (m-30) cc_final: 0.7244 (p0) REVERT: G 322 GLU cc_start: 0.7521 (tt0) cc_final: 0.7121 (tp30) REVERT: H 282 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8789 (pt) REVERT: H 351 LEU cc_start: 0.8566 (mp) cc_final: 0.8326 (mp) outliers start: 40 outliers final: 25 residues processed: 228 average time/residue: 0.3669 time to fit residues: 132.4442 Evaluate side-chains 218 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.0050 chunk 292 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 325 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 0.0040 chunk 170 optimal weight: 4.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25408 Z= 0.127 Angle : 0.430 4.872 34568 Z= 0.224 Chirality : 0.038 0.196 3992 Planarity : 0.003 0.025 4632 Dihedral : 4.135 32.561 3664 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 1.27 % Allowed : 13.02 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3368 helix: 2.40 (0.14), residues: 1328 sheet: -1.05 (0.24), residues: 480 loop : -1.70 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 294 HIS 0.005 0.000 HIS G 363 PHE 0.022 0.002 PHE C 32 TYR 0.017 0.001 TYR E 357 ARG 0.003 0.000 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 2.855 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7972 (pm20) cc_final: 0.7636 (pt0) REVERT: A 326 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7212 (mtm180) REVERT: C 47 GLU cc_start: 0.8004 (pm20) cc_final: 0.7608 (pt0) REVERT: C 119 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7548 (mttm) REVERT: C 351 LEU cc_start: 0.8587 (mp) cc_final: 0.8340 (mp) REVERT: D 119 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7693 (mttp) REVERT: D 351 LEU cc_start: 0.8507 (mp) cc_final: 0.8244 (mp) REVERT: E 351 LEU cc_start: 0.8570 (mp) cc_final: 0.8351 (mp) REVERT: F 119 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7675 (mttp) REVERT: F 264 ASP cc_start: 0.7429 (m-30) cc_final: 0.7149 (p0) REVERT: G 119 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7659 (mttp) REVERT: G 145 MET cc_start: 0.8741 (mmm) cc_final: 0.8532 (mmt) REVERT: G 252 THR cc_start: 0.6868 (OUTLIER) cc_final: 0.6630 (t) REVERT: G 264 ASP cc_start: 0.7613 (m-30) cc_final: 0.7344 (p0) REVERT: G 322 GLU cc_start: 0.7513 (tt0) cc_final: 0.7121 (tp30) REVERT: G 351 LEU cc_start: 0.8687 (mp) cc_final: 0.8449 (mp) REVERT: H 351 LEU cc_start: 0.8535 (mp) cc_final: 0.8298 (mp) outliers start: 32 outliers final: 23 residues processed: 224 average time/residue: 0.3790 time to fit residues: 132.8447 Evaluate side-chains 214 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.0070 chunk 36 optimal weight: 5.9990 chunk 185 optimal weight: 0.0670 chunk 237 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 273 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 323 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25408 Z= 0.288 Angle : 0.489 4.723 34568 Z= 0.255 Chirality : 0.041 0.190 3992 Planarity : 0.004 0.029 4632 Dihedral : 4.266 30.334 3664 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.11 % Allowed : 13.89 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3368 helix: 2.17 (0.14), residues: 1328 sheet: -1.07 (0.24), residues: 480 loop : -1.66 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 294 HIS 0.007 0.001 HIS G 363 PHE 0.022 0.003 PHE H 269 TYR 0.013 0.001 TYR C 357 ARG 0.002 0.000 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 2.611 Fit side-chains REVERT: A 326 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7142 (mtm180) REVERT: C 47 GLU cc_start: 0.8031 (pm20) cc_final: 0.7682 (pt0) REVERT: D 119 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7657 (mttp) REVERT: E 282 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8881 (pt) REVERT: E 351 LEU cc_start: 0.8661 (mp) cc_final: 0.8407 (mp) REVERT: F 119 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7678 (mttp) REVERT: F 264 ASP cc_start: 0.7475 (m-30) cc_final: 0.7125 (p0) REVERT: G 119 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7677 (mttp) REVERT: G 252 THR cc_start: 0.6728 (OUTLIER) cc_final: 0.6494 (t) REVERT: G 322 GLU cc_start: 0.7540 (tt0) cc_final: 0.7150 (tp30) REVERT: H 282 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8816 (pt) outliers start: 28 outliers final: 22 residues processed: 208 average time/residue: 0.3831 time to fit residues: 125.2477 Evaluate side-chains 206 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 30 optimal weight: 0.0570 chunk 254 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25408 Z= 0.155 Angle : 0.436 4.461 34568 Z= 0.226 Chirality : 0.039 0.145 3992 Planarity : 0.003 0.026 4632 Dihedral : 4.095 26.616 3664 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.27 % Allowed : 14.17 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3368 helix: 2.45 (0.14), residues: 1328 sheet: -0.94 (0.24), residues: 480 loop : -1.59 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 294 HIS 0.005 0.000 HIS G 363 PHE 0.029 0.002 PHE A 269 TYR 0.012 0.001 TYR C 357 ARG 0.002 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 2.796 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7987 (pm20) cc_final: 0.7625 (pt0) REVERT: A 326 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7085 (mtm180) REVERT: C 47 GLU cc_start: 0.8004 (pm20) cc_final: 0.7644 (pt0) REVERT: C 119 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7569 (mttm) REVERT: C 351 LEU cc_start: 0.8644 (mp) cc_final: 0.8412 (mp) REVERT: D 119 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7687 (mttp) REVERT: D 145 MET cc_start: 0.8840 (mmm) cc_final: 0.8571 (mmt) REVERT: D 351 LEU cc_start: 0.8542 (mp) cc_final: 0.8319 (mp) REVERT: E 282 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8892 (pt) REVERT: E 351 LEU cc_start: 0.8634 (mp) cc_final: 0.8390 (mp) REVERT: F 119 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7661 (mttp) REVERT: F 264 ASP cc_start: 0.7474 (m-30) cc_final: 0.7151 (p0) REVERT: G 119 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7656 (mttp) REVERT: G 252 THR cc_start: 0.6855 (OUTLIER) cc_final: 0.6619 (t) REVERT: G 264 ASP cc_start: 0.7530 (m-30) cc_final: 0.7251 (p0) REVERT: G 322 GLU cc_start: 0.7499 (tt0) cc_final: 0.7107 (tp30) REVERT: G 351 LEU cc_start: 0.8690 (mp) cc_final: 0.8464 (mp) REVERT: H 282 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8820 (pt) REVERT: H 351 LEU cc_start: 0.8617 (mp) cc_final: 0.8376 (mp) outliers start: 32 outliers final: 25 residues processed: 211 average time/residue: 0.3703 time to fit residues: 122.5563 Evaluate side-chains 212 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 283 optimal weight: 0.9980 chunk 301 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25408 Z= 0.285 Angle : 0.486 4.669 34568 Z= 0.254 Chirality : 0.041 0.175 3992 Planarity : 0.004 0.030 4632 Dihedral : 4.211 25.224 3664 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 1.27 % Allowed : 14.53 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3368 helix: 2.29 (0.14), residues: 1328 sheet: -0.99 (0.24), residues: 480 loop : -1.59 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 294 HIS 0.007 0.001 HIS G 363 PHE 0.027 0.003 PHE D 269 TYR 0.017 0.001 TYR B 357 ARG 0.002 0.000 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 2.769 Fit side-chains REVERT: A 326 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7071 (mtm180) REVERT: C 47 GLU cc_start: 0.8003 (pm20) cc_final: 0.7645 (pt0) REVERT: D 119 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7692 (mttp) REVERT: E 282 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8893 (pt) REVERT: E 351 LEU cc_start: 0.8664 (mp) cc_final: 0.8419 (mp) REVERT: F 119 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7669 (mttp) REVERT: G 119 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7667 (mttp) REVERT: G 252 THR cc_start: 0.6794 (OUTLIER) cc_final: 0.6566 (t) REVERT: G 322 GLU cc_start: 0.7500 (tt0) cc_final: 0.7093 (tp30) REVERT: H 282 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8824 (pt) REVERT: H 351 LEU cc_start: 0.8615 (mp) cc_final: 0.8360 (mp) outliers start: 32 outliers final: 27 residues processed: 205 average time/residue: 0.3851 time to fit residues: 124.6213 Evaluate side-chains 211 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 221 optimal weight: 0.7980 chunk 334 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 266 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25408 Z= 0.219 Angle : 0.463 4.904 34568 Z= 0.241 Chirality : 0.040 0.175 3992 Planarity : 0.003 0.030 4632 Dihedral : 4.187 23.760 3664 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.23 % Allowed : 14.77 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3368 helix: 2.36 (0.14), residues: 1328 sheet: -0.83 (0.24), residues: 472 loop : -1.57 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 294 HIS 0.006 0.001 HIS G 363 PHE 0.034 0.002 PHE A 269 TYR 0.018 0.001 TYR G 357 ARG 0.003 0.000 ARG G 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 2.591 Fit side-chains REVERT: A 47 GLU cc_start: 0.7960 (pm20) cc_final: 0.7702 (pt0) REVERT: A 326 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7060 (mtm180) REVERT: C 47 GLU cc_start: 0.7991 (pm20) cc_final: 0.7627 (pt0) REVERT: C 119 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7710 (mttp) REVERT: C 351 LEU cc_start: 0.8635 (mp) cc_final: 0.8380 (mp) REVERT: D 119 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7680 (mttp) REVERT: D 145 MET cc_start: 0.8854 (mmm) cc_final: 0.8607 (mmt) REVERT: E 282 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8903 (pt) REVERT: E 351 LEU cc_start: 0.8642 (mp) cc_final: 0.8392 (mp) REVERT: F 119 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7653 (mttp) REVERT: G 119 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7648 (mttp) REVERT: G 252 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6687 (t) REVERT: G 322 GLU cc_start: 0.7462 (tt0) cc_final: 0.7051 (tp30) REVERT: G 351 LEU cc_start: 0.8714 (mp) cc_final: 0.8490 (mp) REVERT: H 282 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8831 (pt) REVERT: H 351 LEU cc_start: 0.8610 (mp) cc_final: 0.8368 (mp) outliers start: 31 outliers final: 27 residues processed: 211 average time/residue: 0.3759 time to fit residues: 123.8885 Evaluate side-chains 211 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.0970 chunk 283 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 245 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 266 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 274 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104653 restraints weight = 37932.041| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.16 r_work: 0.3179 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25408 Z= 0.115 Angle : 0.429 5.082 34568 Z= 0.223 Chirality : 0.038 0.176 3992 Planarity : 0.003 0.027 4632 Dihedral : 3.893 23.112 3664 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.15 % Allowed : 14.89 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3368 helix: 2.71 (0.14), residues: 1328 sheet: -0.42 (0.26), residues: 424 loop : -1.47 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 291 HIS 0.004 0.000 HIS G 363 PHE 0.028 0.002 PHE H 269 TYR 0.007 0.001 TYR A 185 ARG 0.002 0.000 ARG B 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4677.40 seconds wall clock time: 85 minutes 5.14 seconds (5105.14 seconds total)