Starting phenix.real_space_refine on Tue Feb 20 16:28:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5z_22067/02_2024/6x5z_22067_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5z_22067/02_2024/6x5z_22067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5z_22067/02_2024/6x5z_22067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5z_22067/02_2024/6x5z_22067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5z_22067/02_2024/6x5z_22067_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5z_22067/02_2024/6x5z_22067_updated.pdb" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 159 5.16 5 C 18019 2.51 5 N 4810 2.21 5 O 5419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O GLU 56": "OE1" <-> "OE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 69": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "O ARG 91": "NH1" <-> "NH2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O ASP 100": "OD1" <-> "OD2" Residue "O GLU 104": "OE1" <-> "OE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O GLU 117": "OE1" <-> "OE2" Residue "O ASP 121": "OD1" <-> "OD2" Residue "O GLU 122": "OE1" <-> "OE2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ASP 137": "OD1" <-> "OD2" Residue "O GLU 142": "OE1" <-> "OE2" Residue "O GLU 145": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 156": "OE1" <-> "OE2" Residue "O ASP 157": "OD1" <-> "OD2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 167": "NH1" <-> "NH2" Residue "O ASP 175": "OD1" <-> "OD2" Residue "O GLU 180": "OE1" <-> "OE2" Residue "O GLU 187": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 196": "OE1" <-> "OE2" Residue "G PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G GLU 107": "OE1" <-> "OE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 269": "OE1" <-> "OE2" Residue "G PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 317": "OE1" <-> "OE2" Residue "G GLU 374": "OE1" <-> "OE2" Residue "G GLU 379": "OE1" <-> "OE2" Residue "G TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "G TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 504": "OE1" <-> "OE2" Residue "G ASP 522": "OD1" <-> "OD2" Residue "G GLU 535": "OE1" <-> "OE2" Residue "G PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 652": "NH1" <-> "NH2" Residue "G GLU 653": "OE1" <-> "OE2" Residue "G ARG 663": "NH1" <-> "NH2" Residue "G ARG 719": "NH1" <-> "NH2" Residue "G ARG 723": "NH1" <-> "NH2" Residue "G GLU 732": "OE1" <-> "OE2" Residue "G ARG 739": "NH1" <-> "NH2" Residue "G GLU 775": "OE1" <-> "OE2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "P GLU 56": "OE1" <-> "OE2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 62": "OE1" <-> "OE2" Residue "P ASP 66": "OD1" <-> "OD2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P GLU 72": "OE1" <-> "OE2" Residue "P ASP 84": "OD1" <-> "OD2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "P GLU 96": "OE1" <-> "OE2" Residue "P GLU 97": "OE1" <-> "OE2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P ASP 100": "OD1" <-> "OD2" Residue "P GLU 104": "OE1" <-> "OE2" Residue "P GLU 114": "OE1" <-> "OE2" Residue "P GLU 115": "OE1" <-> "OE2" Residue "P ASP 121": "OD1" <-> "OD2" Residue "P GLU 122": "OE1" <-> "OE2" Residue "P GLU 131": "OE1" <-> "OE2" Residue "P ASP 137": "OD1" <-> "OD2" Residue "P GLU 138": "OE1" <-> "OE2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "P GLU 145": "OE1" <-> "OE2" Residue "P GLU 150": "OE1" <-> "OE2" Residue "P ASP 157": "OD1" <-> "OD2" Residue "P GLU 163": "OE1" <-> "OE2" Residue "P GLU 180": "OE1" <-> "OE2" Residue "P GLU 184": "OE1" <-> "OE2" Residue "P GLU 187": "OE1" <-> "OE2" Residue "P GLU 192": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 196": "OE1" <-> "OE2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D ASP 522": "OD1" <-> "OD2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 652": "NH1" <-> "NH2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D ARG 663": "NH1" <-> "NH2" Residue "D ARG 719": "NH1" <-> "NH2" Residue "D ARG 723": "NH1" <-> "NH2" Residue "D GLU 732": "OE1" <-> "OE2" Residue "D ARG 739": "NH1" <-> "NH2" Residue "D GLU 775": "OE1" <-> "OE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "J PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 179": "OE1" <-> "OE2" Residue "J ARG 190": "NH1" <-> "NH2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J GLU 269": "OE1" <-> "OE2" Residue "J PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 317": "OE1" <-> "OE2" Residue "J GLU 374": "OE1" <-> "OE2" Residue "J GLU 379": "OE1" <-> "OE2" Residue "J TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 403": "NH1" <-> "NH2" Residue "J TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 434": "NH1" <-> "NH2" Residue "J PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 504": "OE1" <-> "OE2" Residue "J ASP 522": "OD1" <-> "OD2" Residue "J GLU 535": "OE1" <-> "OE2" Residue "J PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 652": "NH1" <-> "NH2" Residue "J GLU 653": "OE1" <-> "OE2" Residue "J ARG 663": "NH1" <-> "NH2" Residue "J ARG 719": "NH1" <-> "NH2" Residue "J ARG 723": "NH1" <-> "NH2" Residue "J GLU 732": "OE1" <-> "OE2" Residue "J ARG 739": "NH1" <-> "NH2" Residue "J GLU 775": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28416 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "O" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "G" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5680 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 2 Chain: "P" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "A" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "D" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5680 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 2 Chain: "C" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "J" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5680 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.37, per 1000 atoms: 0.54 Number of scatterers: 28416 At special positions: 0 Unit cell: (159, 124.02, 248.04, 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 159 16.00 P 6 15.00 Mg 3 11.99 O 5419 8.00 N 4810 7.00 C 18019 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.36 Conformation dependent library (CDL) restraints added in 5.5 seconds 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 30 sheets defined 47.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.916A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 114 through 125 removed outlier: 4.632A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.504A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.651A pdb=" N THR B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 4.100A pdb=" N ARG B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.532A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.667A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 209 removed outlier: 4.175A pdb=" N GLN O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 110 Processing helix chain 'G' and resid 132 through 134 No H-bonds generated for 'chain 'G' and resid 132 through 134' Processing helix chain 'G' and resid 136 through 139 No H-bonds generated for 'chain 'G' and resid 136 through 139' Processing helix chain 'G' and resid 154 through 168 Processing helix chain 'G' and resid 180 through 182 No H-bonds generated for 'chain 'G' and resid 180 through 182' Processing helix chain 'G' and resid 188 through 197 removed outlier: 4.206A pdb=" N GLN G 193 " --> pdb=" O LYS G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 227 removed outlier: 3.971A pdb=" N ALA G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Proline residue: G 225 - end of helix No H-bonds generated for 'chain 'G' and resid 219 through 227' Processing helix chain 'G' and resid 270 through 273 removed outlier: 4.057A pdb=" N VAL G 273 " --> pdb=" O LYS G 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 270 through 273' Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 295 through 301 Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 311 through 315 removed outlier: 3.805A pdb=" N GLN G 315 " --> pdb=" O ALA G 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 311 through 315' Processing helix chain 'G' and resid 325 through 338 removed outlier: 4.778A pdb=" N MET G 330 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA G 331 " --> pdb=" O GLU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 361 removed outlier: 3.795A pdb=" N TYR G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY G 360 " --> pdb=" O ILE G 356 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN G 361 " --> pdb=" O MET G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 387 Processing helix chain 'G' and resid 392 through 400 Processing helix chain 'G' and resid 417 through 447 removed outlier: 3.743A pdb=" N GLY G 425 " --> pdb=" O VAL G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 503 removed outlier: 3.722A pdb=" N LEU G 485 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN G 486 " --> pdb=" O ASN G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 525 removed outlier: 4.065A pdb=" N ALA G 519 " --> pdb=" O ASP G 516 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP G 522 " --> pdb=" O ALA G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 539 removed outlier: 3.594A pdb=" N MET G 539 " --> pdb=" O GLU G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 556 removed outlier: 3.612A pdb=" N LYS G 549 " --> pdb=" O ASP G 545 " (cutoff:3.500A) Processing helix chain 'G' and resid 593 through 597 Processing helix chain 'G' and resid 603 through 610 removed outlier: 4.214A pdb=" N LYS G 610 " --> pdb=" O VAL G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 620 Processing helix chain 'G' and resid 647 through 663 Processing helix chain 'G' and resid 686 through 696 removed outlier: 4.095A pdb=" N HIS G 691 " --> pdb=" O PRO G 687 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 707 Processing helix chain 'G' and resid 715 through 721 Processing helix chain 'G' and resid 738 through 740 No H-bonds generated for 'chain 'G' and resid 738 through 740' Processing helix chain 'G' and resid 772 through 775 No H-bonds generated for 'chain 'G' and resid 772 through 775' Processing helix chain 'P' and resid 46 through 209 removed outlier: 3.651A pdb=" N VAL P 170 " --> pdb=" O ALA P 166 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.917A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 114 through 125 removed outlier: 4.633A pdb=" N GLN A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.504A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.651A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 4.101A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 293 No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.531A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.667A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 154 through 168 Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 188 through 197 removed outlier: 4.206A pdb=" N GLN D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 227 removed outlier: 3.971A pdb=" N ALA D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Proline residue: D 225 - end of helix No H-bonds generated for 'chain 'D' and resid 219 through 227' Processing helix chain 'D' and resid 270 through 273 removed outlier: 4.056A pdb=" N VAL D 273 " --> pdb=" O LYS D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 295 through 301 Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 311 through 315 removed outlier: 3.806A pdb=" N GLN D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 311 through 315' Processing helix chain 'D' and resid 325 through 338 removed outlier: 4.778A pdb=" N MET D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.795A pdb=" N TYR D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN D 361 " --> pdb=" O MET D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 392 through 400 Processing helix chain 'D' and resid 417 through 447 removed outlier: 3.744A pdb=" N GLY D 425 " --> pdb=" O VAL D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 503 removed outlier: 3.722A pdb=" N LEU D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 525 removed outlier: 4.066A pdb=" N ALA D 519 " --> pdb=" O ASP D 516 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D 522 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 539 removed outlier: 3.594A pdb=" N MET D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 556 removed outlier: 3.612A pdb=" N LYS D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 597 Processing helix chain 'D' and resid 603 through 610 removed outlier: 4.215A pdb=" N LYS D 610 " --> pdb=" O VAL D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 647 through 663 Processing helix chain 'D' and resid 686 through 696 removed outlier: 4.095A pdb=" N HIS D 691 " --> pdb=" O PRO D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 707 Processing helix chain 'D' and resid 715 through 721 Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 772 through 775 No H-bonds generated for 'chain 'D' and resid 772 through 775' Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.916A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 114 through 125 removed outlier: 4.632A pdb=" N GLN C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.504A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.651A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 4.100A pdb=" N ARG C 210 " --> pdb=" O ARG C 206 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 293 No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.532A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.668A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 110 Processing helix chain 'J' and resid 132 through 134 No H-bonds generated for 'chain 'J' and resid 132 through 134' Processing helix chain 'J' and resid 136 through 139 No H-bonds generated for 'chain 'J' and resid 136 through 139' Processing helix chain 'J' and resid 154 through 168 Processing helix chain 'J' and resid 180 through 182 No H-bonds generated for 'chain 'J' and resid 180 through 182' Processing helix chain 'J' and resid 188 through 197 removed outlier: 4.206A pdb=" N GLN J 193 " --> pdb=" O LYS J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 227 removed outlier: 3.971A pdb=" N ALA J 223 " --> pdb=" O GLN J 219 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN J 224 " --> pdb=" O ILE J 220 " (cutoff:3.500A) Proline residue: J 225 - end of helix No H-bonds generated for 'chain 'J' and resid 219 through 227' Processing helix chain 'J' and resid 270 through 273 removed outlier: 4.057A pdb=" N VAL J 273 " --> pdb=" O LYS J 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 270 through 273' Processing helix chain 'J' and resid 284 through 290 Processing helix chain 'J' and resid 295 through 301 Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 311 through 315 removed outlier: 3.805A pdb=" N GLN J 315 " --> pdb=" O ALA J 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 311 through 315' Processing helix chain 'J' and resid 325 through 338 removed outlier: 4.777A pdb=" N MET J 330 " --> pdb=" O ALA J 326 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 361 removed outlier: 3.795A pdb=" N TYR J 350 " --> pdb=" O LYS J 346 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY J 360 " --> pdb=" O ILE J 356 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN J 361 " --> pdb=" O MET J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 392 through 400 Processing helix chain 'J' and resid 417 through 447 removed outlier: 3.743A pdb=" N GLY J 425 " --> pdb=" O VAL J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 503 removed outlier: 3.722A pdb=" N LEU J 485 " --> pdb=" O THR J 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN J 486 " --> pdb=" O ASN J 482 " (cutoff:3.500A) Processing helix chain 'J' and resid 513 through 525 removed outlier: 4.066A pdb=" N ALA J 519 " --> pdb=" O ASP J 516 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP J 522 " --> pdb=" O ALA J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 539 removed outlier: 3.594A pdb=" N MET J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 556 removed outlier: 3.612A pdb=" N LYS J 549 " --> pdb=" O ASP J 545 " (cutoff:3.500A) Processing helix chain 'J' and resid 593 through 597 Processing helix chain 'J' and resid 603 through 610 removed outlier: 4.215A pdb=" N LYS J 610 " --> pdb=" O VAL J 606 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 620 Processing helix chain 'J' and resid 647 through 663 Processing helix chain 'J' and resid 686 through 696 removed outlier: 4.096A pdb=" N HIS J 691 " --> pdb=" O PRO J 687 " (cutoff:3.500A) Processing helix chain 'J' and resid 698 through 707 Processing helix chain 'J' and resid 715 through 721 Processing helix chain 'J' and resid 738 through 740 No H-bonds generated for 'chain 'J' and resid 738 through 740' Processing helix chain 'J' and resid 772 through 775 No H-bonds generated for 'chain 'J' and resid 772 through 775' Processing sheet with id= A, first strand: chain 'B' and resid 16 through 19 Processing sheet with id= B, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.733A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 105 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 135 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 107 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 297 through 299 removed outlier: 5.903A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.610A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.613A pdb=" N VAL G 47 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 52 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR G 60 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG G 54 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 116 through 118 Processing sheet with id= H, first strand: chain 'G' and resid 667 through 670 removed outlier: 6.237A pdb=" N SER G 173 " --> pdb=" O HIS G 668 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL G 670 " --> pdb=" O SER G 173 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU G 175 " --> pdb=" O VAL G 670 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE G 250 " --> pdb=" O ILE G 457 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP G 461 " --> pdb=" O LYS G 246 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 363 through 366 removed outlier: 3.853A pdb=" N LYS G 363 " --> pdb=" O ASP G 376 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 577 through 579 Processing sheet with id= K, first strand: chain 'A' and resid 16 through 19 Processing sheet with id= L, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.733A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 105 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 135 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 107 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'A' and resid 297 through 299 removed outlier: 5.903A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.610A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.613A pdb=" N VAL D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 52 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR D 60 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG D 54 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 116 through 118 Processing sheet with id= R, first strand: chain 'D' and resid 667 through 670 removed outlier: 6.237A pdb=" N SER D 173 " --> pdb=" O HIS D 668 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL D 670 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU D 175 " --> pdb=" O VAL D 670 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 250 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 461 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 363 through 366 removed outlier: 3.853A pdb=" N LYS D 363 " --> pdb=" O ASP D 376 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 577 through 579 Processing sheet with id= U, first strand: chain 'C' and resid 16 through 19 Processing sheet with id= V, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.734A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 105 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 135 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 297 through 299 removed outlier: 5.903A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.610A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 37 through 39 removed outlier: 3.613A pdb=" N VAL J 47 " --> pdb=" O VAL J 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU J 52 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR J 60 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG J 54 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 116 through 118 Processing sheet with id= AB, first strand: chain 'J' and resid 667 through 670 removed outlier: 6.237A pdb=" N SER J 173 " --> pdb=" O HIS J 668 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL J 670 " --> pdb=" O SER J 173 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU J 175 " --> pdb=" O VAL J 670 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE J 250 " --> pdb=" O ILE J 457 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP J 461 " --> pdb=" O LYS J 246 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 363 through 366 removed outlier: 3.854A pdb=" N LYS J 363 " --> pdb=" O ASP J 376 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 577 through 579 1189 hydrogen bonds defined for protein. 3333 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: 9.18 Time building geometry restraints manager: 13.15 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: 8990 1.34 - 1.46: 6746 1.46 - 1.58: 12956 1.58 - 1.71: 9 1.71 - 1.83: 277 Bond restraints: 28978 Sorted by residual: bond pdb=" ND1 HIS O 153 " pdb=" CE1 HIS O 153 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.07e+01 bond pdb=" ND1 HIS P 153 " pdb=" CE1 HIS P 153 " ideal model delta sigma weight residual 1.321 1.353 -0.032 1.00e-02 1.00e+04 1.03e+01 bond pdb=" CD ARG P 160 " pdb=" NE ARG P 160 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" CD ARG P 90 " pdb=" NE ARG P 90 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.40e-02 5.10e+03 9.07e+00 bond pdb=" CD ARG O 160 " pdb=" NE ARG O 160 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.40e-02 5.10e+03 8.96e+00 ... (remaining 28973 not shown) Histogram of bond angle deviations from ideal: 93.94 - 102.47: 154 102.47 - 110.99: 10465 110.99 - 119.52: 13984 119.52 - 128.05: 14309 128.05 - 136.58: 196 Bond angle restraints: 39108 Sorted by residual: angle pdb=" C GLY D 708 " pdb=" N PHE D 709 " pdb=" CA PHE D 709 " ideal model delta sigma weight residual 120.09 128.07 -7.98 1.25e+00 6.40e-01 4.08e+01 angle pdb=" C GLY G 708 " pdb=" N PHE G 709 " pdb=" CA PHE G 709 " ideal model delta sigma weight residual 120.09 128.05 -7.96 1.25e+00 6.40e-01 4.06e+01 angle pdb=" C GLY J 708 " pdb=" N PHE J 709 " pdb=" CA PHE J 709 " ideal model delta sigma weight residual 120.09 128.04 -7.95 1.25e+00 6.40e-01 4.05e+01 angle pdb=" N ILE A 287 " pdb=" CA ILE A 287 " pdb=" C ILE A 287 " ideal model delta sigma weight residual 112.29 106.89 5.40 9.40e-01 1.13e+00 3.30e+01 angle pdb=" N ILE C 287 " pdb=" CA ILE C 287 " pdb=" C ILE C 287 " ideal model delta sigma weight residual 112.29 106.89 5.40 9.40e-01 1.13e+00 3.30e+01 ... (remaining 39103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15917 17.98 - 35.96: 1359 35.96 - 53.94: 208 53.94 - 71.92: 93 71.92 - 89.89: 34 Dihedral angle restraints: 17611 sinusoidal: 7259 harmonic: 10352 Sorted by residual: dihedral pdb=" CA ASN C 111 " pdb=" C ASN C 111 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " ideal model delta harmonic sigma weight residual 180.00 147.10 32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ASN B 111 " pdb=" C ASN B 111 " pdb=" N PRO B 112 " pdb=" CA PRO B 112 " ideal model delta harmonic sigma weight residual 180.00 147.10 32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ASN A 111 " pdb=" C ASN A 111 " pdb=" N PRO A 112 " pdb=" CA PRO A 112 " ideal model delta harmonic sigma weight residual 180.00 147.17 32.83 0 5.00e+00 4.00e-02 4.31e+01 ... (remaining 17608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3238 0.055 - 0.110: 856 0.110 - 0.165: 152 0.165 - 0.220: 33 0.220 - 0.276: 11 Chirality restraints: 4290 Sorted by residual: chirality pdb=" CA THR O 108 " pdb=" N THR O 108 " pdb=" C THR O 108 " pdb=" CB THR O 108 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ARG O 182 " pdb=" N ARG O 182 " pdb=" C ARG O 182 " pdb=" CB ARG O 182 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA THR P 201 " pdb=" N THR P 201 " pdb=" C THR P 201 " pdb=" CB THR P 201 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4287 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 162 " 0.104 2.00e-02 2.50e+03 5.34e-02 5.71e+01 pdb=" CG TYR P 162 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR P 162 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR P 162 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR P 162 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR P 162 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR P 162 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR P 162 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 356 " -0.034 2.00e-02 2.50e+03 2.97e-02 2.21e+01 pdb=" CG TRP C 356 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP C 356 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 356 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 356 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 356 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 356 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 356 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 356 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 356 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 356 " -0.034 2.00e-02 2.50e+03 2.97e-02 2.21e+01 pdb=" CG TRP B 356 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 356 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 356 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 356 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 356 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 356 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 356 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 356 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 356 " -0.004 2.00e-02 2.50e+03 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 14 1.85 - 2.61: 479 2.61 - 3.38: 41403 3.38 - 4.14: 65434 4.14 - 4.90: 116171 Nonbonded interactions: 223501 Sorted by model distance: nonbonded pdb=" CG2 VAL P 95 " pdb=" NH2 ARG D 369 " model vdw 1.091 3.540 nonbonded pdb=" NE2 GLN O 93 " pdb=" CD GLN D 368 " model vdw 1.154 3.350 nonbonded pdb=" OD2 ASP B 244 " pdb=" CG2 ILE A 287 " model vdw 1.215 3.460 nonbonded pdb=" OE1 GLN O 93 " pdb=" OE1 GLN D 368 " model vdw 1.315 3.040 nonbonded pdb=" O VAL B 45 " pdb=" OH TYR A 143 " model vdw 1.378 2.440 ... (remaining 223496 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' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'O' selection = chain 'P' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.020 Extract box with map and model: 5.110 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 77.240 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 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 : 0.008 0.071 28978 Z= 0.500 Angle : 1.072 9.366 39108 Z= 0.651 Chirality : 0.053 0.276 4290 Planarity : 0.007 0.129 5058 Dihedral : 14.747 89.894 10935 Min Nonbonded Distance : 1.091 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.29 % Favored : 89.45 % Rotamer: Outliers : 0.10 % Allowed : 1.04 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % Twisted General : 0.18 % 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: -1.68 (0.13), residues: 3526 helix: 0.02 (0.12), residues: 1552 sheet: -1.22 (0.30), residues: 306 loop : -2.24 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.004 TRP C 356 HIS 0.014 0.002 HIS D 651 PHE 0.024 0.003 PHE J 540 TYR 0.104 0.003 TYR P 162 ARG 0.020 0.001 ARG D 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1026 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ILE cc_start: 0.8812 (mt) cc_final: 0.8529 (mt) REVERT: B 87 HIS cc_start: 0.8865 (t70) cc_final: 0.8594 (t-90) REVERT: B 94 LEU cc_start: 0.8202 (tt) cc_final: 0.7962 (mp) REVERT: B 148 THR cc_start: 0.8919 (t) cc_final: 0.8547 (m) REVERT: B 334 GLU cc_start: 0.6320 (mm-30) cc_final: 0.5912 (mt-10) REVERT: B 364 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6802 (mm-30) REVERT: G 90 MET cc_start: 0.6630 (mmt) cc_final: 0.5755 (mmm) REVERT: G 218 ASP cc_start: 0.8042 (m-30) cc_final: 0.7718 (m-30) REVERT: G 295 PRO cc_start: 0.8400 (Cg_endo) cc_final: 0.8083 (Cg_exo) REVERT: G 427 LEU cc_start: 0.8868 (tt) cc_final: 0.8596 (tp) REVERT: G 435 MET cc_start: 0.8868 (ttt) cc_final: 0.8587 (ttm) REVERT: G 478 ILE cc_start: 0.8165 (mm) cc_final: 0.7895 (mm) REVERT: G 523 LEU cc_start: 0.8856 (tp) cc_final: 0.8488 (tp) REVERT: G 616 MET cc_start: 0.7202 (mtm) cc_final: 0.6977 (mtt) REVERT: G 687 PRO cc_start: 0.7875 (Cg_exo) cc_final: 0.7673 (Cg_endo) REVERT: G 704 ILE cc_start: 0.8806 (mm) cc_final: 0.8589 (mm) REVERT: G 745 LEU cc_start: 0.2387 (mt) cc_final: 0.2052 (pt) REVERT: A 244 ASP cc_start: 0.8375 (m-30) cc_final: 0.7546 (t0) REVERT: D 189 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7538 (mptt) REVERT: D 379 GLU cc_start: 0.7528 (pm20) cc_final: 0.7083 (pp20) REVERT: D 435 MET cc_start: 0.7581 (ttt) cc_final: 0.7255 (ttp) REVERT: D 502 LYS cc_start: 0.7454 (tmtt) cc_final: 0.7151 (mmmt) REVERT: D 547 THR cc_start: 0.8392 (p) cc_final: 0.8181 (t) REVERT: D 569 ILE cc_start: 0.6126 (pt) cc_final: 0.5868 (mm) REVERT: D 669 PHE cc_start: 0.5570 (m-80) cc_final: 0.4788 (m-80) REVERT: D 709 PHE cc_start: 0.1863 (m-80) cc_final: 0.1208 (m-10) REVERT: C 87 HIS cc_start: 0.7945 (t70) cc_final: 0.7627 (t-90) REVERT: C 178 LEU cc_start: 0.8714 (tp) cc_final: 0.8339 (pp) REVERT: C 296 ASN cc_start: 0.7866 (m-40) cc_final: 0.7501 (m-40) REVERT: C 323 SER cc_start: 0.8332 (p) cc_final: 0.7748 (t) REVERT: J 76 VAL cc_start: 0.7478 (t) cc_final: 0.7120 (p) REVERT: J 90 MET cc_start: 0.5474 (mmt) cc_final: 0.5022 (mmm) REVERT: J 218 ASP cc_start: 0.7300 (m-30) cc_final: 0.6611 (p0) REVERT: J 295 PRO cc_start: 0.8542 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: J 347 ASN cc_start: 0.6961 (p0) cc_final: 0.6712 (p0) REVERT: J 353 THR cc_start: 0.7907 (m) cc_final: 0.7490 (p) REVERT: J 357 MET cc_start: 0.7540 (mtt) cc_final: 0.7323 (mtt) REVERT: J 563 PHE cc_start: 0.7072 (t80) cc_final: 0.6823 (t80) REVERT: J 657 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8543 (mtpt) outliers start: 3 outliers final: 0 residues processed: 1027 average time/residue: 0.4251 time to fit residues: 663.2045 Evaluate side-chains 570 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 7.9990 chunk 265 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 166 optimal weight: 0.0870 chunk 204 optimal weight: 9.9990 chunk 317 optimal weight: 1.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 144 GLN G 153 HIS ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 GLN G 361 ASN ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 492 HIS G 661 ASN ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN P 153 HIS ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN D 126 ASN D 187 ASN D 251 HIS D 284 HIS D 288 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 246 GLN C 280 ASN C 314 GLN C 371 HIS J 78 GLN J 126 ASN ** J 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN J 251 HIS ** J 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 ASN ** J 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 661 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28978 Z= 0.244 Angle : 0.772 10.052 39108 Z= 0.397 Chirality : 0.047 0.260 4290 Planarity : 0.006 0.079 5058 Dihedral : 6.901 69.916 3867 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.37 % Favored : 92.37 % Rotamer: Outliers : 0.33 % Allowed : 6.16 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3526 helix: 0.42 (0.12), residues: 1593 sheet: -1.02 (0.27), residues: 399 loop : -2.18 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP J 593 HIS 0.013 0.002 HIS J 97 PHE 0.030 0.002 PHE D 669 TYR 0.028 0.002 TYR P 60 ARG 0.010 0.001 ARG J 706 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 756 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 THR cc_start: 0.8939 (t) cc_final: 0.8616 (m) REVERT: B 169 TYR cc_start: 0.8186 (m-80) cc_final: 0.7722 (m-10) REVERT: B 227 MET cc_start: 0.8209 (tpt) cc_final: 0.7944 (tpp) REVERT: B 279 TYR cc_start: 0.8577 (t80) cc_final: 0.8290 (t80) REVERT: B 283 MET cc_start: 0.8928 (mmm) cc_final: 0.8439 (mmt) REVERT: B 334 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6183 (mt-10) REVERT: B 364 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6669 (mm-30) REVERT: G 90 MET cc_start: 0.6179 (mmt) cc_final: 0.5809 (mmm) REVERT: G 98 GLU cc_start: 0.6063 (tt0) cc_final: 0.5484 (tt0) REVERT: G 116 THR cc_start: 0.8331 (m) cc_final: 0.7755 (t) REVERT: G 126 ASN cc_start: 0.8114 (m-40) cc_final: 0.7745 (m-40) REVERT: G 295 PRO cc_start: 0.8532 (Cg_endo) cc_final: 0.8150 (Cg_exo) REVERT: G 473 PHE cc_start: 0.8782 (t80) cc_final: 0.8547 (t80) REVERT: G 704 ILE cc_start: 0.8732 (mm) cc_final: 0.8493 (mm) REVERT: G 745 LEU cc_start: 0.2056 (mt) cc_final: 0.1716 (pt) REVERT: A 93 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7200 (mm-30) REVERT: A 211 ASP cc_start: 0.6393 (m-30) cc_final: 0.6009 (m-30) REVERT: A 225 ASN cc_start: 0.7796 (m110) cc_final: 0.7552 (m110) REVERT: A 244 ASP cc_start: 0.8379 (m-30) cc_final: 0.7169 (t0) REVERT: A 270 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6559 (mt-10) REVERT: A 287 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 325 MET cc_start: 0.8525 (mmp) cc_final: 0.8290 (mmp) REVERT: D 189 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7556 (mmtm) REVERT: D 244 PHE cc_start: 0.7460 (p90) cc_final: 0.6500 (p90) REVERT: D 362 MET cc_start: 0.8943 (mmp) cc_final: 0.8576 (mmm) REVERT: D 368 GLN cc_start: 0.8120 (mt0) cc_final: 0.7817 (pm20) REVERT: D 379 GLU cc_start: 0.7465 (pm20) cc_final: 0.6967 (pp20) REVERT: D 435 MET cc_start: 0.7726 (ttt) cc_final: 0.6988 (ttp) REVERT: D 502 LYS cc_start: 0.7404 (tmtt) cc_final: 0.7160 (mmmt) REVERT: D 547 THR cc_start: 0.8444 (p) cc_final: 0.8105 (t) REVERT: C 47 MET cc_start: 0.7979 (ptp) cc_final: 0.6110 (ptp) REVERT: C 87 HIS cc_start: 0.7863 (t70) cc_final: 0.7601 (t-90) REVERT: C 147 ARG cc_start: 0.5950 (mtp85) cc_final: 0.5484 (mtp85) REVERT: C 323 SER cc_start: 0.8120 (p) cc_final: 0.7705 (t) REVERT: J 218 ASP cc_start: 0.6936 (m-30) cc_final: 0.6409 (p0) REVERT: J 390 LEU cc_start: 0.7836 (tt) cc_final: 0.7151 (tt) REVERT: J 546 MET cc_start: 0.6869 (mtm) cc_final: 0.6667 (mtm) REVERT: J 563 PHE cc_start: 0.7340 (t80) cc_final: 0.7086 (t80) REVERT: J 612 SER cc_start: 0.5474 (m) cc_final: 0.4909 (p) outliers start: 10 outliers final: 3 residues processed: 765 average time/residue: 0.3983 time to fit residues: 482.0001 Evaluate side-chains 531 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 527 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 318 optimal weight: 7.9990 chunk 343 optimal weight: 9.9990 chunk 283 optimal weight: 20.0000 chunk 315 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 ASN ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 ASN ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS A 314 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS D 78 GLN D 187 ASN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 HIS D 661 ASN D 691 HIS ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS J 126 ASN ** J 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 HIS ** J 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 691 HIS ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 28978 Z= 0.392 Angle : 0.838 13.291 39108 Z= 0.431 Chirality : 0.049 0.293 4290 Planarity : 0.006 0.127 5058 Dihedral : 6.861 65.729 3867 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.62 % Favored : 91.18 % Rotamer: Outliers : 0.20 % Allowed : 5.61 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.96 % Twisted General : 0.06 % 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: -1.22 (0.14), residues: 3526 helix: 0.42 (0.13), residues: 1552 sheet: -0.86 (0.27), residues: 372 loop : -2.08 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 340 HIS 0.012 0.002 HIS D 651 PHE 0.042 0.003 PHE G 669 TYR 0.044 0.003 TYR J 722 ARG 0.015 0.001 ARG O 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 642 time to evaluate : 3.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 HIS cc_start: 0.8756 (t-90) cc_final: 0.8483 (t-90) REVERT: B 148 THR cc_start: 0.8973 (t) cc_final: 0.8716 (m) REVERT: B 184 ASP cc_start: 0.8169 (m-30) cc_final: 0.7843 (m-30) REVERT: B 227 MET cc_start: 0.8034 (tpt) cc_final: 0.7690 (tpp) REVERT: B 283 MET cc_start: 0.8961 (mmm) cc_final: 0.8710 (mmt) REVERT: B 362 TYR cc_start: 0.8245 (t80) cc_final: 0.7910 (t80) REVERT: B 364 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6917 (mm-30) REVERT: G 90 MET cc_start: 0.6470 (mmt) cc_final: 0.6059 (mmm) REVERT: G 98 GLU cc_start: 0.5992 (tt0) cc_final: 0.4961 (tt0) REVERT: G 126 ASN cc_start: 0.8373 (m-40) cc_final: 0.7945 (m-40) REVERT: G 174 ILE cc_start: 0.8885 (mp) cc_final: 0.8634 (mt) REVERT: G 244 PHE cc_start: 0.9095 (p90) cc_final: 0.8474 (p90) REVERT: G 295 PRO cc_start: 0.8572 (Cg_endo) cc_final: 0.8170 (Cg_exo) REVERT: G 704 ILE cc_start: 0.8591 (mm) cc_final: 0.8377 (mm) REVERT: G 745 LEU cc_start: 0.2231 (mt) cc_final: 0.1612 (pt) REVERT: A 166 TYR cc_start: 0.8495 (t80) cc_final: 0.8222 (t80) REVERT: A 244 ASP cc_start: 0.8033 (m-30) cc_final: 0.6818 (t0) REVERT: A 325 MET cc_start: 0.8652 (mmp) cc_final: 0.8254 (mmp) REVERT: D 189 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7546 (mmtm) REVERT: D 244 PHE cc_start: 0.7825 (p90) cc_final: 0.6916 (p90) REVERT: D 341 PHE cc_start: 0.7634 (m-80) cc_final: 0.7214 (m-80) REVERT: D 346 LYS cc_start: 0.8177 (tmtt) cc_final: 0.7968 (tttp) REVERT: D 362 MET cc_start: 0.9036 (mmp) cc_final: 0.8628 (mmt) REVERT: D 368 GLN cc_start: 0.8246 (mt0) cc_final: 0.7936 (pm20) REVERT: D 379 GLU cc_start: 0.7619 (pm20) cc_final: 0.7103 (pp20) REVERT: D 435 MET cc_start: 0.7547 (ttt) cc_final: 0.7170 (ttp) REVERT: D 502 LYS cc_start: 0.7454 (tmtt) cc_final: 0.7021 (mmmt) REVERT: D 721 ARG cc_start: 0.7216 (mtt180) cc_final: 0.6838 (mtp180) REVERT: C 262 PHE cc_start: 0.8852 (m-80) cc_final: 0.8603 (m-10) REVERT: C 323 SER cc_start: 0.7969 (p) cc_final: 0.7610 (t) REVERT: J 218 ASP cc_start: 0.7142 (m-30) cc_final: 0.6464 (p0) REVERT: J 357 MET cc_start: 0.8063 (mtt) cc_final: 0.7296 (mtm) REVERT: J 669 PHE cc_start: 0.7711 (m-80) cc_final: 0.7493 (m-80) outliers start: 6 outliers final: 1 residues processed: 647 average time/residue: 0.4082 time to fit residues: 414.8715 Evaluate side-chains 472 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 471 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 338 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 302 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 471 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 314 GLN C 371 HIS J 126 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN J 491 HIS ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28978 Z= 0.227 Angle : 0.725 12.563 39108 Z= 0.368 Chirality : 0.046 0.300 4290 Planarity : 0.005 0.125 5058 Dihedral : 6.539 66.977 3867 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.46 % Favored : 92.40 % Rotamer: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.96 % Twisted General : 0.03 % 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: -0.87 (0.14), residues: 3526 helix: 0.80 (0.13), residues: 1539 sheet: -0.84 (0.27), residues: 366 loop : -1.92 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP J 438 HIS 0.009 0.001 HIS D 492 PHE 0.031 0.002 PHE G 669 TYR 0.026 0.002 TYR J 287 ARG 0.007 0.001 ARG J 706 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 674 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 HIS cc_start: 0.8619 (t-90) cc_final: 0.8415 (t-90) REVERT: B 148 THR cc_start: 0.9099 (t) cc_final: 0.8714 (m) REVERT: B 227 MET cc_start: 0.8081 (tpt) cc_final: 0.7768 (tpp) REVERT: B 283 MET cc_start: 0.8986 (mmm) cc_final: 0.8612 (mmt) REVERT: B 362 TYR cc_start: 0.8125 (t80) cc_final: 0.7857 (t80) REVERT: B 364 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6795 (mm-30) REVERT: G 90 MET cc_start: 0.6162 (mmt) cc_final: 0.5710 (mmm) REVERT: G 98 GLU cc_start: 0.5657 (tt0) cc_final: 0.5372 (tt0) REVERT: G 174 ILE cc_start: 0.8969 (mp) cc_final: 0.8554 (mm) REVERT: G 248 ILE cc_start: 0.7857 (mm) cc_final: 0.7527 (mm) REVERT: G 269 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7195 (mm-30) REVERT: G 295 PRO cc_start: 0.8539 (Cg_endo) cc_final: 0.8087 (Cg_exo) REVERT: G 497 GLU cc_start: 0.7540 (tp30) cc_final: 0.7332 (tp30) REVERT: G 704 ILE cc_start: 0.8615 (mm) cc_final: 0.8255 (mm) REVERT: G 707 LYS cc_start: 0.8477 (ptpp) cc_final: 0.7832 (ptpp) REVERT: G 745 LEU cc_start: 0.2773 (mt) cc_final: 0.1976 (pt) REVERT: P 127 MET cc_start: 0.4086 (ptt) cc_final: 0.3844 (ptt) REVERT: A 205 GLU cc_start: 0.7252 (pt0) cc_final: 0.7027 (mt-10) REVERT: A 211 ASP cc_start: 0.6368 (m-30) cc_final: 0.6034 (m-30) REVERT: A 244 ASP cc_start: 0.7939 (m-30) cc_final: 0.6766 (t0) REVERT: A 270 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6666 (mt-10) REVERT: A 325 MET cc_start: 0.8643 (mmp) cc_final: 0.8224 (mmp) REVERT: D 77 LEU cc_start: 0.7591 (tp) cc_final: 0.7351 (tp) REVERT: D 189 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7559 (mmtm) REVERT: D 244 PHE cc_start: 0.7694 (p90) cc_final: 0.7047 (p90) REVERT: D 341 PHE cc_start: 0.7201 (m-80) cc_final: 0.6994 (m-80) REVERT: D 357 MET cc_start: 0.8631 (mtt) cc_final: 0.7858 (mpp) REVERT: D 362 MET cc_start: 0.8996 (mmp) cc_final: 0.8495 (mmt) REVERT: D 379 GLU cc_start: 0.7530 (pm20) cc_final: 0.7102 (pp20) REVERT: D 435 MET cc_start: 0.7613 (ttt) cc_final: 0.7174 (ttp) REVERT: D 489 PHE cc_start: 0.6827 (t80) cc_final: 0.6179 (t80) REVERT: D 499 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8627 (tm-30) REVERT: D 502 LYS cc_start: 0.7366 (tmtt) cc_final: 0.6917 (mmmt) REVERT: D 547 THR cc_start: 0.8332 (p) cc_final: 0.7986 (t) REVERT: D 669 PHE cc_start: 0.5457 (m-10) cc_final: 0.5253 (m-10) REVERT: D 690 MET cc_start: 0.7047 (ppp) cc_final: 0.6508 (tpp) REVERT: D 721 ARG cc_start: 0.7223 (mtt180) cc_final: 0.6784 (mtp180) REVERT: C 205 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7442 (mp0) REVERT: C 296 ASN cc_start: 0.7694 (m-40) cc_final: 0.7351 (m110) REVERT: C 323 SER cc_start: 0.7975 (p) cc_final: 0.7426 (t) REVERT: C 352 PHE cc_start: 0.7234 (t80) cc_final: 0.6691 (t80) REVERT: J 218 ASP cc_start: 0.7097 (m-30) cc_final: 0.6361 (p0) REVERT: J 288 GLN cc_start: 0.6798 (mt0) cc_final: 0.6273 (mp10) REVERT: J 357 MET cc_start: 0.7800 (mtt) cc_final: 0.6964 (mtm) REVERT: J 433 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7637 (tm-30) REVERT: J 466 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7989 (mm-30) REVERT: J 612 SER cc_start: 0.6577 (m) cc_final: 0.6351 (p) outliers start: 3 outliers final: 1 residues processed: 676 average time/residue: 0.4059 time to fit residues: 431.7203 Evaluate side-chains 498 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 497 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 50.0000 chunk 192 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 ASN ** G 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 314 GLN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 HIS ** J 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28978 Z= 0.266 Angle : 0.739 11.281 39108 Z= 0.378 Chirality : 0.047 0.286 4290 Planarity : 0.005 0.124 5058 Dihedral : 6.435 63.334 3867 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.94 % Favored : 91.97 % Rotamer: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.48 % 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: -0.89 (0.14), residues: 3526 helix: 0.74 (0.13), residues: 1554 sheet: -0.82 (0.27), residues: 369 loop : -1.92 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 340 HIS 0.011 0.002 HIS D 492 PHE 0.025 0.002 PHE G 669 TYR 0.023 0.002 TYR J 715 ARG 0.009 0.001 ARG J 706 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 627 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 HIS cc_start: 0.8605 (t-90) cc_final: 0.8391 (t-90) REVERT: B 227 MET cc_start: 0.7994 (tpt) cc_final: 0.7464 (tmm) REVERT: B 283 MET cc_start: 0.8964 (mmm) cc_final: 0.8709 (mmt) REVERT: B 340 TRP cc_start: 0.9244 (t60) cc_final: 0.8675 (t60) REVERT: B 362 TYR cc_start: 0.8188 (t80) cc_final: 0.7942 (t80) REVERT: O 154 ILE cc_start: 0.4987 (pt) cc_final: 0.4713 (pt) REVERT: G 98 GLU cc_start: 0.5886 (tt0) cc_final: 0.5408 (tt0) REVERT: G 102 LEU cc_start: 0.7910 (mt) cc_final: 0.7703 (mt) REVERT: G 174 ILE cc_start: 0.8850 (mp) cc_final: 0.8529 (mt) REVERT: G 248 ILE cc_start: 0.7930 (mm) cc_final: 0.7680 (mm) REVERT: G 295 PRO cc_start: 0.8430 (Cg_endo) cc_final: 0.7989 (Cg_exo) REVERT: G 704 ILE cc_start: 0.8586 (mm) cc_final: 0.8328 (mm) REVERT: G 745 LEU cc_start: 0.2936 (mt) cc_final: 0.2099 (pt) REVERT: A 205 GLU cc_start: 0.7108 (pt0) cc_final: 0.6870 (mt-10) REVERT: A 211 ASP cc_start: 0.6269 (m-30) cc_final: 0.6030 (m-30) REVERT: A 244 ASP cc_start: 0.7665 (m-30) cc_final: 0.6605 (t0) REVERT: D 97 HIS cc_start: 0.6774 (m170) cc_final: 0.6213 (m170) REVERT: D 189 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7478 (mmtm) REVERT: D 244 PHE cc_start: 0.7736 (p90) cc_final: 0.6975 (p90) REVERT: D 341 PHE cc_start: 0.7105 (m-80) cc_final: 0.6868 (m-80) REVERT: D 357 MET cc_start: 0.8756 (mtt) cc_final: 0.7953 (mpp) REVERT: D 362 MET cc_start: 0.9007 (mmp) cc_final: 0.8454 (mmt) REVERT: D 369 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6973 (tpt-90) REVERT: D 379 GLU cc_start: 0.7576 (pm20) cc_final: 0.7101 (pp20) REVERT: D 435 MET cc_start: 0.7633 (ttt) cc_final: 0.7185 (ttp) REVERT: D 499 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8573 (tm-30) REVERT: D 502 LYS cc_start: 0.7467 (tmtt) cc_final: 0.6980 (mmmt) REVERT: D 534 LEU cc_start: 0.8531 (tp) cc_final: 0.8048 (tp) REVERT: D 547 THR cc_start: 0.8326 (p) cc_final: 0.7911 (t) REVERT: D 721 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6850 (mtp180) REVERT: C 120 THR cc_start: 0.9405 (t) cc_final: 0.9195 (t) REVERT: C 132 MET cc_start: 0.8413 (tmm) cc_final: 0.8170 (tmm) REVERT: C 205 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7545 (mp0) REVERT: C 323 SER cc_start: 0.7979 (p) cc_final: 0.7502 (t) REVERT: C 370 VAL cc_start: 0.8791 (p) cc_final: 0.8570 (t) REVERT: J 218 ASP cc_start: 0.7252 (m-30) cc_final: 0.6406 (p0) REVERT: J 357 MET cc_start: 0.7954 (mtt) cc_final: 0.7238 (mtt) REVERT: J 433 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7564 (tm-30) REVERT: J 466 GLU cc_start: 0.8212 (mm-30) cc_final: 0.8008 (mm-30) outliers start: 1 outliers final: 0 residues processed: 628 average time/residue: 0.4072 time to fit residues: 401.9394 Evaluate side-chains 465 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 1.9990 chunk 304 optimal weight: 0.0270 chunk 66 optimal weight: 8.9990 chunk 198 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 314 GLN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN J 187 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 HIS ** J 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 661 ASN ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28978 Z= 0.242 Angle : 0.721 11.081 39108 Z= 0.367 Chirality : 0.046 0.294 4290 Planarity : 0.005 0.118 5058 Dihedral : 6.313 62.330 3867 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.95 % Rotamer: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.72 (0.14), residues: 3526 helix: 0.94 (0.13), residues: 1524 sheet: -0.77 (0.27), residues: 372 loop : -1.84 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP C 340 HIS 0.015 0.001 HIS D 492 PHE 0.022 0.002 PHE G 669 TYR 0.023 0.002 TYR G 422 ARG 0.012 0.001 ARG D 706 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 618 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 TYR cc_start: 0.8073 (m-10) cc_final: 0.7443 (m-10) REVERT: B 279 TYR cc_start: 0.8560 (t80) cc_final: 0.8278 (t80) REVERT: B 325 MET cc_start: 0.7686 (mmt) cc_final: 0.7369 (mmm) REVERT: B 340 TRP cc_start: 0.9249 (t60) cc_final: 0.9044 (t60) REVERT: B 362 TYR cc_start: 0.8194 (t80) cc_final: 0.7914 (t80) REVERT: O 154 ILE cc_start: 0.4909 (pt) cc_final: 0.4672 (pt) REVERT: G 98 GLU cc_start: 0.5587 (tt0) cc_final: 0.5026 (tt0) REVERT: G 174 ILE cc_start: 0.8960 (mp) cc_final: 0.8580 (mt) REVERT: G 248 ILE cc_start: 0.8008 (mm) cc_final: 0.7696 (mt) REVERT: G 265 THR cc_start: 0.7470 (m) cc_final: 0.7147 (p) REVERT: G 295 PRO cc_start: 0.8474 (Cg_endo) cc_final: 0.8030 (Cg_exo) REVERT: G 745 LEU cc_start: 0.2706 (mt) cc_final: 0.1915 (pt) REVERT: G 770 LEU cc_start: 0.1929 (mt) cc_final: 0.1469 (mt) REVERT: A 120 THR cc_start: 0.8775 (t) cc_final: 0.8507 (t) REVERT: A 244 ASP cc_start: 0.7518 (m-30) cc_final: 0.6450 (t0) REVERT: A 299 MET cc_start: 0.7562 (mpp) cc_final: 0.7252 (mpp) REVERT: A 325 MET cc_start: 0.8446 (mmp) cc_final: 0.8173 (mmp) REVERT: A 334 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6705 (mt-10) REVERT: D 162 TYR cc_start: 0.6592 (t80) cc_final: 0.6363 (t80) REVERT: D 189 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7484 (mmtm) REVERT: D 244 PHE cc_start: 0.7192 (p90) cc_final: 0.6910 (p90) REVERT: D 341 PHE cc_start: 0.7416 (m-80) cc_final: 0.7172 (m-80) REVERT: D 357 MET cc_start: 0.8564 (mtt) cc_final: 0.7763 (mpp) REVERT: D 362 MET cc_start: 0.9004 (mmp) cc_final: 0.8511 (mmt) REVERT: D 369 ARG cc_start: 0.7476 (mtt180) cc_final: 0.6958 (tpt-90) REVERT: D 435 MET cc_start: 0.7425 (ttt) cc_final: 0.7147 (ttp) REVERT: D 499 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8503 (tm-30) REVERT: D 502 LYS cc_start: 0.7575 (tmtt) cc_final: 0.7200 (mmtt) REVERT: D 506 ILE cc_start: 0.4881 (mt) cc_final: 0.4414 (mt) REVERT: D 547 THR cc_start: 0.8288 (p) cc_final: 0.7862 (t) REVERT: D 721 ARG cc_start: 0.7113 (mtt180) cc_final: 0.6753 (mtp180) REVERT: C 120 THR cc_start: 0.9399 (t) cc_final: 0.9181 (t) REVERT: C 205 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7604 (mp0) REVERT: J 218 ASP cc_start: 0.7278 (m-30) cc_final: 0.6360 (p0) REVERT: J 357 MET cc_start: 0.8002 (mtt) cc_final: 0.7177 (mtt) REVERT: J 427 LEU cc_start: 0.8720 (pp) cc_final: 0.8255 (pp) REVERT: J 433 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7643 (tm-30) REVERT: J 466 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7985 (mm-30) REVERT: J 535 GLU cc_start: 0.6772 (tp30) cc_final: 0.6504 (tp30) REVERT: J 598 LYS cc_start: 0.7953 (mttt) cc_final: 0.7565 (mttp) outliers start: 2 outliers final: 1 residues processed: 620 average time/residue: 0.3922 time to fit residues: 385.2031 Evaluate side-chains 475 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 474 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 337 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 HIS A 88 HIS A 314 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS ** J 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 GLN J 240 ASN J 347 ASN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28978 Z= 0.323 Angle : 0.754 10.632 39108 Z= 0.387 Chirality : 0.048 0.313 4290 Planarity : 0.006 0.135 5058 Dihedral : 6.418 59.791 3867 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.48 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.48 % Twisted General : 0.03 % 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: -0.91 (0.14), residues: 3526 helix: 0.69 (0.13), residues: 1542 sheet: -0.78 (0.27), residues: 372 loop : -1.87 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.004 TRP C 340 HIS 0.016 0.002 HIS D 492 PHE 0.051 0.002 PHE G 669 TYR 0.023 0.002 TYR D 103 ARG 0.007 0.001 ARG J 706 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8215 (ptp) cc_final: 0.7088 (tpt) REVERT: B 82 MET cc_start: 0.8267 (tpt) cc_final: 0.7761 (tpt) REVERT: B 132 MET cc_start: 0.8837 (ppp) cc_final: 0.8586 (ptm) REVERT: B 279 TYR cc_start: 0.8561 (t80) cc_final: 0.8142 (t80) REVERT: B 340 TRP cc_start: 0.9316 (t60) cc_final: 0.9068 (t60) REVERT: B 362 TYR cc_start: 0.8240 (t80) cc_final: 0.7979 (t80) REVERT: B 364 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6876 (mm-30) REVERT: G 98 GLU cc_start: 0.5829 (tt0) cc_final: 0.5228 (tt0) REVERT: G 102 LEU cc_start: 0.8018 (mt) cc_final: 0.7744 (mt) REVERT: G 174 ILE cc_start: 0.8947 (mp) cc_final: 0.8550 (mt) REVERT: G 248 ILE cc_start: 0.8200 (mm) cc_final: 0.7936 (mt) REVERT: G 295 PRO cc_start: 0.8482 (Cg_endo) cc_final: 0.8055 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8874 (mmpt) cc_final: 0.8595 (mmmm) REVERT: G 413 LYS cc_start: 0.7906 (mttt) cc_final: 0.7498 (mmtp) REVERT: G 745 LEU cc_start: 0.2697 (mt) cc_final: 0.1864 (pt) REVERT: G 770 LEU cc_start: 0.1962 (mt) cc_final: 0.1657 (mt) REVERT: A 244 ASP cc_start: 0.7288 (m-30) cc_final: 0.6417 (t0) REVERT: A 270 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6624 (mt-10) REVERT: A 325 MET cc_start: 0.8503 (mmp) cc_final: 0.8262 (mmp) REVERT: D 162 TYR cc_start: 0.6844 (t80) cc_final: 0.6463 (t80) REVERT: D 189 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7551 (mmtm) REVERT: D 325 ASP cc_start: 0.7973 (m-30) cc_final: 0.7675 (t0) REVERT: D 341 PHE cc_start: 0.7568 (m-80) cc_final: 0.7322 (m-80) REVERT: D 357 MET cc_start: 0.8682 (mtt) cc_final: 0.7951 (mpp) REVERT: D 362 MET cc_start: 0.8980 (mmp) cc_final: 0.8473 (mmt) REVERT: D 369 ARG cc_start: 0.7778 (mtt180) cc_final: 0.6951 (tpt-90) REVERT: D 435 MET cc_start: 0.7526 (ttt) cc_final: 0.7267 (ttp) REVERT: D 499 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8572 (tm-30) REVERT: D 502 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7247 (mmtt) REVERT: D 547 THR cc_start: 0.8523 (p) cc_final: 0.8113 (t) REVERT: D 549 LYS cc_start: 0.8933 (ptmm) cc_final: 0.8732 (tttt) REVERT: D 721 ARG cc_start: 0.6982 (mtt180) cc_final: 0.6605 (mtp180) REVERT: C 205 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7754 (mp0) REVERT: C 352 PHE cc_start: 0.7158 (t80) cc_final: 0.6853 (t80) REVERT: J 357 MET cc_start: 0.8020 (mtt) cc_final: 0.7123 (mtt) REVERT: J 433 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7621 (tm-30) REVERT: J 528 MET cc_start: 0.7614 (tpt) cc_final: 0.7264 (tpt) REVERT: J 535 GLU cc_start: 0.6870 (tp30) cc_final: 0.6548 (tp30) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.3944 time to fit residues: 378.4192 Evaluate side-chains 465 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 358 HIS ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN D 361 ASN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28978 Z= 0.293 Angle : 0.753 10.044 39108 Z= 0.386 Chirality : 0.047 0.308 4290 Planarity : 0.005 0.127 5058 Dihedral : 6.434 58.623 3867 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.54 % Favored : 91.38 % Rotamer: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3526 helix: 0.64 (0.13), residues: 1560 sheet: -0.75 (0.27), residues: 378 loop : -1.97 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.004 TRP C 340 HIS 0.014 0.002 HIS D 492 PHE 0.034 0.002 PHE G 669 TYR 0.023 0.002 TYR A 166 ARG 0.008 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 599 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.7078 (ptp) cc_final: 0.6777 (tpt) REVERT: B 82 MET cc_start: 0.8323 (tpt) cc_final: 0.7848 (tpt) REVERT: B 148 THR cc_start: 0.9217 (t) cc_final: 0.9003 (m) REVERT: B 325 MET cc_start: 0.7902 (mmt) cc_final: 0.7543 (mmt) REVERT: B 362 TYR cc_start: 0.8244 (t80) cc_final: 0.7942 (t80) REVERT: G 92 MET cc_start: 0.8235 (mmp) cc_final: 0.7800 (mmp) REVERT: G 98 GLU cc_start: 0.5747 (tt0) cc_final: 0.5180 (tt0) REVERT: G 102 LEU cc_start: 0.8089 (mt) cc_final: 0.7834 (mt) REVERT: G 174 ILE cc_start: 0.8946 (mp) cc_final: 0.8550 (mt) REVERT: G 248 ILE cc_start: 0.8221 (mm) cc_final: 0.7932 (mt) REVERT: G 295 PRO cc_start: 0.8406 (Cg_endo) cc_final: 0.8017 (Cg_exo) REVERT: G 363 LYS cc_start: 0.8902 (mmpt) cc_final: 0.8636 (mmmm) REVERT: G 745 LEU cc_start: 0.2642 (mt) cc_final: 0.1885 (pt) REVERT: P 143 ILE cc_start: 0.7394 (pt) cc_final: 0.7170 (mm) REVERT: P 178 ARG cc_start: 0.4706 (mmp-170) cc_final: 0.4493 (mmp-170) REVERT: A 244 ASP cc_start: 0.7295 (m-30) cc_final: 0.6509 (t0) REVERT: A 270 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6601 (mt-10) REVERT: A 325 MET cc_start: 0.8668 (mmp) cc_final: 0.8403 (mmp) REVERT: D 135 ASN cc_start: 0.4316 (p0) cc_final: 0.4051 (p0) REVERT: D 153 HIS cc_start: 0.6604 (t70) cc_final: 0.6199 (t70) REVERT: D 189 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7497 (mmtm) REVERT: D 325 ASP cc_start: 0.7914 (m-30) cc_final: 0.7583 (t0) REVERT: D 341 PHE cc_start: 0.7671 (m-80) cc_final: 0.7438 (m-80) REVERT: D 357 MET cc_start: 0.8712 (mtt) cc_final: 0.7874 (mpp) REVERT: D 362 MET cc_start: 0.8915 (mmp) cc_final: 0.8394 (mmt) REVERT: D 369 ARG cc_start: 0.7785 (mtt180) cc_final: 0.6717 (tpt-90) REVERT: D 499 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8588 (tm-30) REVERT: D 502 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7222 (mmtt) REVERT: D 709 PHE cc_start: 0.1861 (m-10) cc_final: 0.1401 (m-10) REVERT: C 125 GLU cc_start: 0.6330 (mm-30) cc_final: 0.5622 (mm-30) REVERT: C 205 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7753 (mp0) REVERT: C 305 MET cc_start: 0.7361 (mpp) cc_final: 0.6955 (mtt) REVERT: C 313 MET cc_start: 0.8790 (mmm) cc_final: 0.8465 (mmm) REVERT: C 352 PHE cc_start: 0.7336 (t80) cc_final: 0.6992 (t80) REVERT: C 362 TYR cc_start: 0.5768 (t80) cc_final: 0.5529 (t80) REVERT: J 357 MET cc_start: 0.8019 (mtt) cc_final: 0.7046 (mtt) REVERT: J 433 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7605 (tm-30) REVERT: J 528 MET cc_start: 0.7717 (tpt) cc_final: 0.7322 (tpt) REVERT: J 535 GLU cc_start: 0.6986 (tp30) cc_final: 0.6665 (tp30) outliers start: 1 outliers final: 1 residues processed: 599 average time/residue: 0.4005 time to fit residues: 378.5908 Evaluate side-chains 459 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 458 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 0.9980 chunk 323 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 246 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 284 optimal weight: 8.9990 chunk 297 optimal weight: 0.0570 chunk 313 optimal weight: 6.9990 overall best weight: 1.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 314 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 GLN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28978 Z= 0.221 Angle : 0.732 11.003 39108 Z= 0.371 Chirality : 0.046 0.295 4290 Planarity : 0.005 0.129 5058 Dihedral : 6.244 56.954 3867 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.88 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.03 % 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: -0.86 (0.14), residues: 3526 helix: 0.72 (0.13), residues: 1527 sheet: -0.64 (0.27), residues: 378 loop : -1.86 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.004 TRP C 340 HIS 0.016 0.001 HIS D 492 PHE 0.037 0.002 PHE G 669 TYR 0.022 0.002 TYR J 287 ARG 0.007 0.001 ARG O 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 627 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.8162 (ttt) cc_final: 0.7837 (ttt) REVERT: B 47 MET cc_start: 0.6966 (ptp) cc_final: 0.6312 (tpt) REVERT: B 82 MET cc_start: 0.8273 (tpt) cc_final: 0.7870 (tpt) REVERT: B 279 TYR cc_start: 0.8547 (t80) cc_final: 0.8053 (t80) REVERT: B 325 MET cc_start: 0.7779 (mmt) cc_final: 0.7495 (mmt) REVERT: B 334 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6546 (mt-10) REVERT: B 340 TRP cc_start: 0.8975 (t60) cc_final: 0.8671 (t60) REVERT: B 362 TYR cc_start: 0.8200 (t80) cc_final: 0.7858 (t80) REVERT: G 98 GLU cc_start: 0.5490 (tt0) cc_final: 0.5157 (tt0) REVERT: G 174 ILE cc_start: 0.8961 (mp) cc_final: 0.8544 (mt) REVERT: G 248 ILE cc_start: 0.8165 (mm) cc_final: 0.7856 (mt) REVERT: G 295 PRO cc_start: 0.8356 (Cg_endo) cc_final: 0.8000 (Cg_exo) REVERT: G 334 ASN cc_start: 0.8513 (t0) cc_final: 0.8293 (t0) REVERT: G 363 LYS cc_start: 0.8938 (mmpt) cc_final: 0.8672 (mmmm) REVERT: G 371 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8125 (pm20) REVERT: G 590 ILE cc_start: 0.8702 (pt) cc_final: 0.8333 (pt) REVERT: G 704 ILE cc_start: 0.8526 (mm) cc_final: 0.8295 (mm) REVERT: G 707 LYS cc_start: 0.8618 (ptpp) cc_final: 0.8352 (pttt) REVERT: G 745 LEU cc_start: 0.2766 (mt) cc_final: 0.2038 (pt) REVERT: A 205 GLU cc_start: 0.7774 (pt0) cc_final: 0.7071 (mt-10) REVERT: A 244 ASP cc_start: 0.7151 (m-30) cc_final: 0.6336 (t0) REVERT: A 270 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6549 (mt-10) REVERT: A 325 MET cc_start: 0.8579 (mmp) cc_final: 0.8291 (mmp) REVERT: D 189 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7482 (mmtm) REVERT: D 307 PRO cc_start: 0.7835 (Cg_endo) cc_final: 0.7554 (Cg_exo) REVERT: D 341 PHE cc_start: 0.7757 (m-80) cc_final: 0.7445 (m-80) REVERT: D 357 MET cc_start: 0.8697 (mtt) cc_final: 0.7904 (mpp) REVERT: D 362 MET cc_start: 0.8935 (mmp) cc_final: 0.8342 (mmt) REVERT: D 369 ARG cc_start: 0.7858 (mtt180) cc_final: 0.6575 (ttt-90) REVERT: D 435 MET cc_start: 0.7739 (ttp) cc_final: 0.7478 (ttp) REVERT: D 499 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8576 (tm-30) REVERT: D 502 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7231 (mmtt) REVERT: D 512 ASP cc_start: 0.7419 (m-30) cc_final: 0.7173 (m-30) REVERT: D 534 LEU cc_start: 0.8632 (tp) cc_final: 0.8209 (tp) REVERT: D 547 THR cc_start: 0.8342 (p) cc_final: 0.7875 (t) REVERT: C 107 GLU cc_start: 0.7990 (tp30) cc_final: 0.7483 (tp30) REVERT: C 125 GLU cc_start: 0.6423 (mm-30) cc_final: 0.5876 (mm-30) REVERT: C 205 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7679 (mp0) REVERT: C 305 MET cc_start: 0.7264 (mpp) cc_final: 0.6823 (mtt) REVERT: C 362 TYR cc_start: 0.5751 (t80) cc_final: 0.5535 (t80) REVERT: J 46 PHE cc_start: 0.5580 (m-80) cc_final: 0.4938 (m-10) REVERT: J 357 MET cc_start: 0.7918 (mtt) cc_final: 0.6992 (mtt) REVERT: J 422 TYR cc_start: 0.7926 (m-10) cc_final: 0.7594 (m-10) REVERT: J 433 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7479 (tm-30) REVERT: J 528 MET cc_start: 0.7778 (tpt) cc_final: 0.7274 (tpt) REVERT: J 535 GLU cc_start: 0.6910 (tp30) cc_final: 0.6483 (tp30) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.3967 time to fit residues: 392.9758 Evaluate side-chains 471 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 10.0000 chunk 332 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 320 optimal weight: 4.9990 chunk 277 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 170 optimal weight: 0.5980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28978 Z= 0.235 Angle : 0.742 10.753 39108 Z= 0.376 Chirality : 0.046 0.324 4290 Planarity : 0.005 0.130 5058 Dihedral : 6.221 54.829 3867 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.86 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3526 helix: 0.68 (0.13), residues: 1528 sheet: -0.47 (0.27), residues: 372 loop : -1.83 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.004 TRP C 340 HIS 0.016 0.001 HIS D 492 PHE 0.039 0.002 PHE G 195 TYR 0.025 0.002 TYR B 198 ARG 0.008 0.001 ARG O 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 604 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.8161 (ttt) cc_final: 0.7818 (ttt) REVERT: B 47 MET cc_start: 0.7059 (ptp) cc_final: 0.6146 (tpp) REVERT: B 82 MET cc_start: 0.8334 (tpt) cc_final: 0.7950 (tpt) REVERT: B 325 MET cc_start: 0.7825 (mmt) cc_final: 0.7614 (mmp) REVERT: B 334 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6535 (mt-10) REVERT: B 362 TYR cc_start: 0.8186 (t80) cc_final: 0.7784 (t80) REVERT: O 127 MET cc_start: 0.4712 (mpp) cc_final: 0.4278 (mmm) REVERT: G 98 GLU cc_start: 0.5492 (tt0) cc_final: 0.5217 (tt0) REVERT: G 174 ILE cc_start: 0.8952 (mp) cc_final: 0.8626 (mt) REVERT: G 248 ILE cc_start: 0.8119 (mm) cc_final: 0.7880 (mt) REVERT: G 295 PRO cc_start: 0.8353 (Cg_endo) cc_final: 0.7955 (Cg_exo) REVERT: G 334 ASN cc_start: 0.8507 (t0) cc_final: 0.8271 (t0) REVERT: G 363 LYS cc_start: 0.8971 (mmpt) cc_final: 0.8692 (mmmm) REVERT: G 590 ILE cc_start: 0.8724 (pt) cc_final: 0.8371 (pt) REVERT: G 704 ILE cc_start: 0.8506 (mm) cc_final: 0.8259 (mm) REVERT: G 707 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8338 (pttt) REVERT: G 745 LEU cc_start: 0.2839 (mt) cc_final: 0.2125 (pt) REVERT: P 143 ILE cc_start: 0.7181 (pt) cc_final: 0.6980 (mm) REVERT: A 244 ASP cc_start: 0.7178 (m-30) cc_final: 0.6414 (t0) REVERT: A 270 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6534 (mt-10) REVERT: A 283 MET cc_start: 0.8495 (mmm) cc_final: 0.8155 (tpp) REVERT: A 325 MET cc_start: 0.8601 (mmp) cc_final: 0.8309 (mmp) REVERT: D 71 VAL cc_start: 0.7328 (p) cc_final: 0.7032 (m) REVERT: D 189 LYS cc_start: 0.7775 (ttpt) cc_final: 0.7438 (mmtm) REVERT: D 307 PRO cc_start: 0.7968 (Cg_endo) cc_final: 0.7493 (Cg_exo) REVERT: D 313 ILE cc_start: 0.7079 (pt) cc_final: 0.6783 (tp) REVERT: D 341 PHE cc_start: 0.7704 (m-80) cc_final: 0.7456 (m-80) REVERT: D 357 MET cc_start: 0.8689 (mtt) cc_final: 0.7911 (mpp) REVERT: D 362 MET cc_start: 0.8876 (mmp) cc_final: 0.8270 (mmt) REVERT: D 369 ARG cc_start: 0.7884 (mtt180) cc_final: 0.6640 (ttt-90) REVERT: D 465 PHE cc_start: 0.7010 (t80) cc_final: 0.6456 (t80) REVERT: D 499 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8557 (tm-30) REVERT: D 502 LYS cc_start: 0.7735 (tmtt) cc_final: 0.7249 (mmtt) REVERT: D 547 THR cc_start: 0.8456 (p) cc_final: 0.8034 (t) REVERT: C 125 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5810 (mm-30) REVERT: C 205 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7715 (mp0) REVERT: C 305 MET cc_start: 0.7328 (mpp) cc_final: 0.6907 (mtt) REVERT: C 362 TYR cc_start: 0.5761 (t80) cc_final: 0.5496 (t80) REVERT: J 357 MET cc_start: 0.7893 (mtt) cc_final: 0.7072 (mtt) REVERT: J 388 MET cc_start: 0.8275 (tmm) cc_final: 0.8050 (tmm) REVERT: J 433 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7575 (tm-30) REVERT: J 528 MET cc_start: 0.7777 (tpt) cc_final: 0.7286 (tpt) outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.3814 time to fit residues: 367.9059 Evaluate side-chains 467 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 256 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 285 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 HIS ** G 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 144 GLN A 314 GLN D 126 ASN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 ASN ** J 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.141545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114556 restraints weight = 75746.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.113418 restraints weight = 73723.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114542 restraints weight = 66251.963| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28978 Z= 0.208 Angle : 0.726 9.820 39108 Z= 0.367 Chirality : 0.046 0.272 4290 Planarity : 0.005 0.128 5058 Dihedral : 6.075 53.295 3867 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3526 helix: 0.76 (0.13), residues: 1522 sheet: -0.53 (0.26), residues: 396 loop : -1.80 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.004 TRP C 340 HIS 0.016 0.001 HIS D 492 PHE 0.039 0.002 PHE D 489 TYR 0.025 0.002 TYR G 310 ARG 0.006 0.001 ARG C 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7119.13 seconds wall clock time: 130 minutes 3.87 seconds (7803.87 seconds total)