Starting phenix.real_space_refine on Mon Apr 15 10:17:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz1_30021/04_2024/6lz1_30021.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz1_30021/04_2024/6lz1_30021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz1_30021/04_2024/6lz1_30021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz1_30021/04_2024/6lz1_30021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz1_30021/04_2024/6lz1_30021.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz1_30021/04_2024/6lz1_30021.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 164 5.16 5 C 22020 2.51 5 N 5808 2.21 5 O 6496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "A GLU 785": "OE1" <-> "OE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 791": "OD1" <-> "OD2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 855": "OE1" <-> "OE2" Residue "A PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 859": "OD1" <-> "OD2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 994": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1045": "OE1" <-> "OE2" Residue "A ASP 1046": "OD1" <-> "OD2" Residue "A ASP 1057": "OD1" <-> "OD2" Residue "A TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B GLU 624": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B ASP 695": "OD1" <-> "OD2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 717": "OD1" <-> "OD2" Residue "B PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 751": "OD1" <-> "OD2" Residue "B GLU 785": "OE1" <-> "OE2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 791": "OD1" <-> "OD2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 855": "OE1" <-> "OE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 859": "OD1" <-> "OD2" Residue "B GLU 863": "OE1" <-> "OE2" Residue "B PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 901": "OD1" <-> "OD2" Residue "B PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 994": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1045": "OE1" <-> "OE2" Residue "B ASP 1046": "OD1" <-> "OD2" Residue "B ASP 1057": "OD1" <-> "OD2" Residue "B TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ASP 249": "OD1" <-> "OD2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 468": "OD1" <-> "OD2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C ASP 604": "OD1" <-> "OD2" Residue "C GLU 624": "OE1" <-> "OE2" Residue "C GLU 664": "OE1" <-> "OE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "C ASP 695": "OD1" <-> "OD2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 717": "OD1" <-> "OD2" Residue "C PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 751": "OD1" <-> "OD2" Residue "C GLU 785": "OE1" <-> "OE2" Residue "C TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 791": "OD1" <-> "OD2" Residue "C GLU 815": "OE1" <-> "OE2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 855": "OE1" <-> "OE2" Residue "C PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 859": "OD1" <-> "OD2" Residue "C GLU 863": "OE1" <-> "OE2" Residue "C PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 901": "OD1" <-> "OD2" Residue "C PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 994": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1045": "OE1" <-> "OE2" Residue "C ASP 1046": "OD1" <-> "OD2" Residue "C ASP 1057": "OD1" <-> "OD2" Residue "C TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 388": "OE1" <-> "OE2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 420": "OD1" <-> "OD2" Residue "D ASP 468": "OD1" <-> "OD2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D ARG 558": "NH1" <-> "NH2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D ASP 604": "OD1" <-> "OD2" Residue "D GLU 624": "OE1" <-> "OE2" Residue "D GLU 664": "OE1" <-> "OE2" Residue "D GLU 682": "OE1" <-> "OE2" Residue "D ASP 695": "OD1" <-> "OD2" Residue "D TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 717": "OD1" <-> "OD2" Residue "D PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "D GLU 785": "OE1" <-> "OE2" Residue "D TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 791": "OD1" <-> "OD2" Residue "D GLU 815": "OE1" <-> "OE2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 855": "OE1" <-> "OE2" Residue "D PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 859": "OD1" <-> "OD2" Residue "D GLU 863": "OE1" <-> "OE2" Residue "D PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 901": "OD1" <-> "OD2" Residue "D PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 994": "OE1" <-> "OE2" Residue "D GLU 1017": "OE1" <-> "OE2" Residue "D GLU 1045": "OE1" <-> "OE2" Residue "D ASP 1046": "OD1" <-> "OD2" Residue "D ASP 1057": "OD1" <-> "OD2" Residue "D TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34492 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8622 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1027} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8622 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1027} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8622 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1027} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8622 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1027} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.39, per 1000 atoms: 0.50 Number of scatterers: 34492 At special positions: 0 Unit cell: (138.32, 98.8, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 164 16.00 O 6496 8.00 N 5808 7.00 C 22020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.62 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 615 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" NE2 HIS B 615 " pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 615 " pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" NE2 HIS D 615 " 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8128 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 48 sheets defined 29.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR A 561 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 592 Processing helix chain 'A' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 653 Proline residue: A 632 - end of helix Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU A 784 " --> pdb=" O VAL A 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 785 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL A 961 " --> pdb=" O ASP A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 224 Processing helix chain 'B' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR B 561 " --> pdb=" O ARG B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 592 Processing helix chain 'B' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 653 Proline residue: B 632 - end of helix Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU B 784 " --> pdb=" O VAL B 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 785 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 887 Processing helix chain 'B' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL B 961 " --> pdb=" O ASP B 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS C 118 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 224 Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 353 Processing helix chain 'C' and resid 372 through 391 Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU C 503 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR C 561 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 592 Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS C 612 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 653 Proline residue: C 632 - end of helix Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU C 784 " --> pdb=" O VAL C 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 785 " --> pdb=" O PHE C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 887 Processing helix chain 'C' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL C 961 " --> pdb=" O ASP C 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS D 118 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 224 Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS D 276 " --> pdb=" O VAL D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 312 " --> pdb=" O ARG D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 353 Processing helix chain 'D' and resid 372 through 391 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU D 503 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR D 561 " --> pdb=" O ARG D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 592 Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 653 Proline residue: D 632 - end of helix Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU D 784 " --> pdb=" O VAL D 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU D 785 " --> pdb=" O PHE D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 887 Processing helix chain 'D' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL D 961 " --> pdb=" O ASP D 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU A 89 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 65 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 133 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 143 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE A 193 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 284 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 489 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 286 " --> pdb=" O PHE A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 283 " --> pdb=" O LYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE A 398 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP A 548 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN A 441 " --> pdb=" O TRP A 548 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG A 972 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU A 666 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 702 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG A 747 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS A 850 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG A 929 " --> pdb=" O LYS A 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 852 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY A 915 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER A 806 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 813 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE A 896 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER A 900 " --> pdb=" O PHE A 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE A 864 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 989 through 993 Processing sheet with id=AB3, first strand: chain 'A' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG A1014 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A1002 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE A1012 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A1072 " --> pdb=" O CYS A1040 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU B 89 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 65 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 133 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 143 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE B 193 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 152 through 154 Processing sheet with id=AB7, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE B 325 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B 326 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 287 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE B 284 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE B 489 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 286 " --> pdb=" O PHE B 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE B 325 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B 326 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 287 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL B 283 " --> pdb=" O LYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE B 398 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP B 548 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN B 441 " --> pdb=" O TRP B 548 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG B 972 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 666 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 702 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG B 747 " --> pdb=" O ASP B 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS B 850 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG B 929 " --> pdb=" O LYS B 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 852 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 915 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER B 806 " --> pdb=" O LYS B 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 813 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE B 896 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER B 900 " --> pdb=" O PHE B 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE B 864 " --> pdb=" O SER B 900 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 989 through 993 Processing sheet with id=AC6, first strand: chain 'B' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG B1014 " --> pdb=" O SER B1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B1002 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B1012 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR B1072 " --> pdb=" O CYS B1040 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU C 89 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 65 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 133 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 143 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE C 193 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 152 through 154 Processing sheet with id=AD1, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 284 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE C 489 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 286 " --> pdb=" O PHE C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C 283 " --> pdb=" O LYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE C 398 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP C 548 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN C 441 " --> pdb=" O TRP C 548 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG C 972 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 666 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 702 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG C 747 " --> pdb=" O ASP C 742 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS C 850 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 929 " --> pdb=" O LYS C 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 852 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY C 915 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER C 806 " --> pdb=" O LYS C 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 813 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 817 " --> pdb=" O ILE C 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 896 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER C 900 " --> pdb=" O PHE C 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE C 864 " --> pdb=" O SER C 900 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 989 through 993 Processing sheet with id=AD9, first strand: chain 'C' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG C1014 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C1002 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C1012 " --> pdb=" O ILE C1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C1072 " --> pdb=" O CYS C1040 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU D 89 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU D 65 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 133 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN D 143 " --> pdb=" O VAL D 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE D 193 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 152 through 154 Processing sheet with id=AE4, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE D 325 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL D 326 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY D 287 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE D 284 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE D 489 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE D 286 " --> pdb=" O PHE D 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE D 325 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL D 326 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY D 287 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 283 " --> pdb=" O LYS D 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE D 398 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP D 548 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN D 441 " --> pdb=" O TRP D 548 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG D 972 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 666 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 702 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG D 747 " --> pdb=" O ASP D 742 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS D 850 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG D 929 " --> pdb=" O LYS D 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D 852 " --> pdb=" O LEU D 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY D 915 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER D 806 " --> pdb=" O LYS D 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 813 " --> pdb=" O SER D 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER D 817 " --> pdb=" O ILE D 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE D 896 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER D 900 " --> pdb=" O PHE D 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE D 864 " --> pdb=" O SER D 900 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 989 through 993 Processing sheet with id=AF3, first strand: chain 'D' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG D1014 " --> pdb=" O SER D1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D1002 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D1012 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR D1072 " --> pdb=" O CYS D1040 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 3996 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: 17.42 Time building geometry restraints manager: 13.80 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: 11232 1.34 - 1.46: 7696 1.46 - 1.58: 16216 1.58 - 1.69: 0 1.69 - 1.81: 232 Bond restraints: 35376 Sorted by residual: bond pdb=" CA GLU C1017 " pdb=" C GLU C1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU D1017 " pdb=" C GLU D1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU A1017 " pdb=" C GLU A1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU B1017 " pdb=" C GLU B1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CG LEU D 264 " pdb=" CD2 LEU D 264 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 35371 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.92: 740 105.92 - 112.95: 18916 112.95 - 119.97: 12052 119.97 - 127.00: 15796 127.00 - 134.03: 516 Bond angle restraints: 48020 Sorted by residual: angle pdb=" N GLN C 425 " pdb=" CA GLN C 425 " pdb=" CB GLN C 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN B 425 " pdb=" CA GLN B 425 " pdb=" CB GLN B 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN D 425 " pdb=" CA GLN D 425 " pdb=" CB GLN D 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN A 425 " pdb=" CA GLN A 425 " pdb=" CB GLN A 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLU C1017 " pdb=" CA GLU C1017 " pdb=" C GLU C1017 " ideal model delta sigma weight residual 110.28 103.28 7.00 1.48e+00 4.57e-01 2.24e+01 ... (remaining 48015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 18284 17.05 - 34.09: 2112 34.09 - 51.14: 424 51.14 - 68.19: 112 68.19 - 85.23: 48 Dihedral angle restraints: 20980 sinusoidal: 8400 harmonic: 12580 Sorted by residual: dihedral pdb=" CA TYR B 42 " pdb=" C TYR B 42 " pdb=" N ASP B 43 " pdb=" CA ASP B 43 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA TYR D 42 " pdb=" C TYR D 42 " pdb=" N ASP D 43 " pdb=" CA ASP D 43 " ideal model delta harmonic sigma weight residual 180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA TYR C 42 " pdb=" C TYR C 42 " pdb=" N ASP C 43 " pdb=" CA ASP C 43 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 20977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3664 0.045 - 0.090: 1176 0.090 - 0.135: 348 0.135 - 0.180: 16 0.180 - 0.225: 8 Chirality restraints: 5212 Sorted by residual: chirality pdb=" CA THR B 903 " pdb=" N THR B 903 " pdb=" C THR B 903 " pdb=" CB THR B 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR D 903 " pdb=" N THR D 903 " pdb=" C THR D 903 " pdb=" CB THR D 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR A 903 " pdb=" N THR A 903 " pdb=" C THR A 903 " pdb=" CB THR A 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5209 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 422 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE D 422 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE D 422 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 423 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 422 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE C 422 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE C 422 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 423 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 422 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE B 422 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE B 422 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 423 " -0.013 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 724 2.66 - 3.22: 32592 3.22 - 3.78: 55422 3.78 - 4.34: 81682 4.34 - 4.90: 135842 Nonbonded interactions: 306262 Sorted by model distance: nonbonded pdb=" OD2 ASP A 402 " pdb="ZN ZN A1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP D 402 " pdb="ZN ZN D1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP B 402 " pdb="ZN ZN B1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP C 402 " pdb="ZN ZN C1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP C 292 " pdb="ZN ZN C1201 " model vdw 2.104 2.230 ... (remaining 306257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 4.870 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 97.220 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 35376 Z= 0.337 Angle : 0.615 7.001 48020 Z= 0.360 Chirality : 0.047 0.225 5212 Planarity : 0.004 0.032 6216 Dihedral : 15.467 85.234 12852 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.52 % Allowed : 17.25 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.11), residues: 4296 helix: -1.18 (0.13), residues: 1172 sheet: -2.09 (0.15), residues: 944 loop : -3.00 (0.11), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 159 HIS 0.004 0.001 HIS B 476 PHE 0.013 0.001 PHE A 97 TYR 0.015 0.001 TYR D 627 ARG 0.003 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 336 time to evaluate : 3.824 Fit side-chains REVERT: A 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7312 (m-40) REVERT: A 1004 MET cc_start: 0.8340 (mmm) cc_final: 0.8113 (tpt) REVERT: B 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7310 (m-40) REVERT: B 1004 MET cc_start: 0.8343 (mmm) cc_final: 0.8117 (tpt) REVERT: C 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7311 (m-40) REVERT: C 1004 MET cc_start: 0.8346 (mmm) cc_final: 0.8117 (tpt) REVERT: D 433 ASN cc_start: 0.7604 (m110) cc_final: 0.7314 (m-40) REVERT: D 1004 MET cc_start: 0.8347 (mmm) cc_final: 0.8117 (tpt) outliers start: 96 outliers final: 72 residues processed: 408 average time/residue: 0.5034 time to fit residues: 340.8666 Evaluate side-chains 364 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 292 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 806 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1046 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 4.9990 chunk 324 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 335 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 266 ASN A 288 HIS A 369 ASN A 412 GLN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS A 458 ASN A 475 GLN A 651 GLN A 675 ASN A 758 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS A 829 ASN A 921 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 ASN ** A1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 266 ASN B 288 HIS B 369 ASN B 412 GLN B 453 HIS B 458 ASN B 475 GLN B 651 GLN B 675 ASN B 758 HIS ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 HIS B 829 ASN B 921 ASN ** B 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 266 ASN C 288 HIS C 369 ASN C 412 GLN C 453 HIS C 458 ASN C 475 GLN C 651 GLN C 675 ASN C 758 HIS ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 HIS C 829 ASN C 921 ASN ** C 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 996 ASN ** C1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1076 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 266 ASN D 288 HIS D 369 ASN D 412 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS D 475 GLN D 651 GLN D 675 ASN D 758 HIS ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 HIS D 829 ASN D 921 ASN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 996 ASN ** D1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1076 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35376 Z= 0.158 Angle : 0.513 5.937 48020 Z= 0.275 Chirality : 0.043 0.134 5212 Planarity : 0.003 0.029 6216 Dihedral : 6.398 50.327 4728 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.58 % Allowed : 16.82 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.12), residues: 4296 helix: 0.13 (0.15), residues: 1192 sheet: -1.75 (0.15), residues: 944 loop : -2.63 (0.11), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 159 HIS 0.005 0.001 HIS B 861 PHE 0.010 0.001 PHE B 782 TYR 0.013 0.001 TYR D 627 ARG 0.006 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 348 time to evaluate : 4.034 Fit side-chains REVERT: A 308 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7659 (ptp90) REVERT: A 1004 MET cc_start: 0.8067 (mmm) cc_final: 0.7840 (tpt) REVERT: B 308 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7659 (ptp90) REVERT: B 1004 MET cc_start: 0.8062 (mmm) cc_final: 0.7837 (tpt) REVERT: C 308 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7658 (ptp90) REVERT: C 1004 MET cc_start: 0.8066 (mmm) cc_final: 0.7839 (tpt) REVERT: D 308 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7661 (ptp90) REVERT: D 1004 MET cc_start: 0.8066 (mmm) cc_final: 0.7839 (tpt) outliers start: 136 outliers final: 64 residues processed: 460 average time/residue: 0.4639 time to fit residues: 356.9538 Evaluate side-chains 368 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 300 time to evaluate : 4.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 216 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 420 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 chunk 386 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 312 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN A 996 ASN ** A1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN B 996 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 HIS ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN C 996 ASN ** C1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 HIS ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 982 ASN D 996 ASN ** D1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35376 Z= 0.278 Angle : 0.547 6.440 48020 Z= 0.290 Chirality : 0.045 0.137 5212 Planarity : 0.004 0.035 6216 Dihedral : 6.024 49.311 4660 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.21 % Allowed : 17.88 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.12), residues: 4296 helix: 0.51 (0.15), residues: 1188 sheet: -1.70 (0.15), residues: 976 loop : -2.45 (0.12), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 159 HIS 0.006 0.001 HIS B 861 PHE 0.016 0.002 PHE D 856 TYR 0.022 0.001 TYR C 627 ARG 0.004 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 316 time to evaluate : 4.463 Fit side-chains REVERT: A 308 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7653 (ptp90) REVERT: A 1001 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.7556 (t-90) REVERT: B 308 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7654 (ptp90) REVERT: B 1001 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.7554 (t-90) REVERT: C 308 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7654 (ptp90) REVERT: C 1001 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.7552 (t-90) REVERT: D 308 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7653 (ptp90) REVERT: D 1001 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.7553 (t-90) outliers start: 160 outliers final: 104 residues processed: 436 average time/residue: 0.4552 time to fit residues: 334.8045 Evaluate side-chains 412 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 300 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1001 HIS Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1001 HIS Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1056 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 384 optimal weight: 0.4980 chunk 292 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 185 optimal weight: 0.8980 chunk 261 optimal weight: 0.4980 chunk 390 optimal weight: 5.9990 chunk 413 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 370 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 412 GLN A 557 HIS A 775 GLN A 982 ASN ** A1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS B 775 GLN B 982 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS C 775 GLN C 982 ASN ** C1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN D 412 GLN D 557 HIS D 775 GLN D 982 ASN ** D1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 35376 Z= 0.135 Angle : 0.486 6.963 48020 Z= 0.258 Chirality : 0.042 0.166 5212 Planarity : 0.003 0.031 6216 Dihedral : 5.638 46.136 4652 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.52 % Allowed : 19.45 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4296 helix: 0.97 (0.15), residues: 1188 sheet: -1.39 (0.15), residues: 992 loop : -2.30 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 159 HIS 0.004 0.001 HIS C 453 PHE 0.011 0.001 PHE C 856 TYR 0.012 0.001 TYR D 627 ARG 0.004 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 368 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1000 SER cc_start: 0.8533 (t) cc_final: 0.8271 (p) REVERT: A 1001 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7418 (t-90) REVERT: B 1000 SER cc_start: 0.8532 (t) cc_final: 0.8269 (p) REVERT: B 1001 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7418 (t-90) REVERT: C 1000 SER cc_start: 0.8532 (t) cc_final: 0.8268 (p) REVERT: C 1001 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7420 (t-90) REVERT: D 1000 SER cc_start: 0.8532 (t) cc_final: 0.8269 (p) REVERT: D 1001 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7419 (t-90) outliers start: 96 outliers final: 64 residues processed: 448 average time/residue: 0.4608 time to fit residues: 346.4261 Evaluate side-chains 387 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 319 time to evaluate : 4.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 1001 HIS Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 1001 HIS Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1056 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 344 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 353 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 HIS ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 HIS ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 HIS ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 894 GLN ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1001 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 35376 Z= 0.376 Angle : 0.579 7.905 48020 Z= 0.307 Chirality : 0.046 0.144 5212 Planarity : 0.004 0.042 6216 Dihedral : 5.759 46.566 4636 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.79 % Allowed : 19.35 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4296 helix: 0.74 (0.15), residues: 1192 sheet: -1.54 (0.15), residues: 940 loop : -2.30 (0.12), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 159 HIS 0.005 0.001 HIS A 476 PHE 0.025 0.002 PHE D 380 TYR 0.030 0.002 TYR C 627 ARG 0.002 0.000 ARG D 924 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 294 time to evaluate : 4.152 Fit side-chains REVERT: A 46 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7198 (ttm-80) REVERT: A 308 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7701 (ptp90) REVERT: A 433 ASN cc_start: 0.7667 (m110) cc_final: 0.7305 (m-40) REVERT: B 46 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7197 (ttm-80) REVERT: B 308 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7704 (ptp90) REVERT: B 433 ASN cc_start: 0.7665 (m110) cc_final: 0.7303 (m-40) REVERT: C 46 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7197 (ttm-80) REVERT: C 308 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7704 (ptp90) REVERT: C 433 ASN cc_start: 0.7668 (m110) cc_final: 0.7306 (m-40) REVERT: D 46 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7196 (ttm-80) REVERT: D 308 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7701 (ptp90) REVERT: D 433 ASN cc_start: 0.7667 (m110) cc_final: 0.7305 (m-40) outliers start: 144 outliers final: 100 residues processed: 414 average time/residue: 0.4636 time to fit residues: 321.0175 Evaluate side-chains 394 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 286 time to evaluate : 5.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1056 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 139 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 414 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN B 982 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 982 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35376 Z= 0.256 Angle : 0.539 9.228 48020 Z= 0.285 Chirality : 0.044 0.132 5212 Planarity : 0.003 0.034 6216 Dihedral : 5.671 44.802 4636 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.60 % Allowed : 19.95 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.12), residues: 4296 helix: 0.86 (0.15), residues: 1188 sheet: -1.44 (0.15), residues: 952 loop : -2.26 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 159 HIS 0.004 0.001 HIS B 861 PHE 0.012 0.001 PHE A 97 TYR 0.010 0.001 TYR D 714 ARG 0.003 0.000 ARG B 924 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 308 time to evaluate : 4.379 Fit side-chains REVERT: A 46 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7146 (ttm-80) REVERT: A 308 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7690 (ptp90) REVERT: A 314 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7220 (mtt) REVERT: A 433 ASN cc_start: 0.7662 (m110) cc_final: 0.7303 (m-40) REVERT: B 46 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7144 (ttm-80) REVERT: B 308 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7694 (ptp90) REVERT: B 314 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7220 (mtt) REVERT: B 433 ASN cc_start: 0.7661 (m110) cc_final: 0.7305 (m-40) REVERT: C 46 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7149 (ttm-80) REVERT: C 308 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7692 (ptp90) REVERT: C 314 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7218 (mtt) REVERT: C 433 ASN cc_start: 0.7665 (m110) cc_final: 0.7306 (m-40) REVERT: D 46 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7149 (ttm-80) REVERT: D 308 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7692 (ptp90) REVERT: D 314 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7220 (mtt) REVERT: D 433 ASN cc_start: 0.7661 (m110) cc_final: 0.7303 (m-40) outliers start: 137 outliers final: 108 residues processed: 413 average time/residue: 0.4763 time to fit residues: 326.0535 Evaluate side-chains 412 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 292 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1056 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 399 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 412 optimal weight: 0.0980 chunk 258 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 921 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35376 Z= 0.208 Angle : 0.523 10.693 48020 Z= 0.276 Chirality : 0.043 0.158 5212 Planarity : 0.003 0.031 6216 Dihedral : 5.576 44.561 4636 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.23 % Allowed : 20.48 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.12), residues: 4296 helix: 0.94 (0.15), residues: 1188 sheet: -1.38 (0.15), residues: 952 loop : -2.20 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 159 HIS 0.003 0.001 HIS B 861 PHE 0.012 0.001 PHE C 856 TYR 0.026 0.001 TYR C 627 ARG 0.002 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 312 time to evaluate : 5.365 Fit side-chains REVERT: A 46 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7114 (ttm-80) REVERT: A 308 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7674 (ptp90) REVERT: A 433 ASN cc_start: 0.7652 (m110) cc_final: 0.7307 (m-40) REVERT: A 681 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 46 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7113 (ttm-80) REVERT: B 308 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7676 (ptp90) REVERT: B 433 ASN cc_start: 0.7657 (m110) cc_final: 0.7307 (m-40) REVERT: B 681 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8484 (p) REVERT: C 46 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7115 (ttm-80) REVERT: C 308 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7677 (ptp90) REVERT: C 433 ASN cc_start: 0.7655 (m110) cc_final: 0.7309 (m-40) REVERT: C 681 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8484 (p) REVERT: D 46 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7114 (ttm-80) REVERT: D 308 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7675 (ptp90) REVERT: D 433 ASN cc_start: 0.7652 (m110) cc_final: 0.7307 (m-40) REVERT: D 681 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8482 (p) outliers start: 123 outliers final: 92 residues processed: 411 average time/residue: 0.4842 time to fit residues: 329.4309 Evaluate side-chains 392 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 288 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1056 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 255 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 81 optimal weight: 0.0980 chunk 79 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 GLN B 982 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 982 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 982 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35376 Z= 0.244 Angle : 0.537 11.326 48020 Z= 0.284 Chirality : 0.044 0.162 5212 Planarity : 0.003 0.033 6216 Dihedral : 5.588 44.335 4636 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.15 % Allowed : 20.48 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 4296 helix: 0.99 (0.15), residues: 1188 sheet: -1.38 (0.15), residues: 952 loop : -2.16 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 159 HIS 0.003 0.001 HIS C 476 PHE 0.014 0.001 PHE B 856 TYR 0.017 0.001 TYR A 627 ARG 0.002 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 288 time to evaluate : 4.199 Fit side-chains REVERT: A 46 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7145 (ttm-80) REVERT: A 308 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7681 (ptp90) REVERT: A 314 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7215 (mtt) REVERT: A 433 ASN cc_start: 0.7658 (m110) cc_final: 0.7302 (m-40) REVERT: B 46 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7143 (ttm-80) REVERT: B 308 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7683 (ptp90) REVERT: B 314 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7214 (mtt) REVERT: B 433 ASN cc_start: 0.7660 (m110) cc_final: 0.7304 (m-40) REVERT: C 46 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7144 (ttm-80) REVERT: C 308 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7681 (ptp90) REVERT: C 314 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7213 (mtt) REVERT: C 433 ASN cc_start: 0.7661 (m110) cc_final: 0.7305 (m-40) REVERT: D 46 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7145 (ttm-80) REVERT: D 308 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7680 (ptp90) REVERT: D 314 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7212 (mtt) REVERT: D 433 ASN cc_start: 0.7656 (m110) cc_final: 0.7302 (m-40) outliers start: 158 outliers final: 123 residues processed: 416 average time/residue: 0.4669 time to fit residues: 323.0042 Evaluate side-chains 419 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 284 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1056 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 375 optimal weight: 0.9990 chunk 395 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 384 optimal weight: 0.6980 chunk 231 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 301 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 363 optimal weight: 2.9990 chunk 383 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 982 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 GLN B 982 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 982 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 GLN D 982 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35376 Z= 0.187 Angle : 0.522 12.501 48020 Z= 0.275 Chirality : 0.043 0.163 5212 Planarity : 0.003 0.030 6216 Dihedral : 5.479 43.716 4636 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.94 % Allowed : 20.77 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 4296 helix: 1.08 (0.15), residues: 1188 sheet: -1.15 (0.15), residues: 964 loop : -2.15 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 159 HIS 0.003 0.001 HIS C 453 PHE 0.012 0.001 PHE B 856 TYR 0.012 0.001 TYR C 627 ARG 0.002 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 294 time to evaluate : 4.651 Fit side-chains REVERT: A 46 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7050 (ttm-80) REVERT: A 308 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7694 (ptp90) REVERT: A 314 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7188 (mtt) REVERT: A 474 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7665 (p0) REVERT: A 681 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 46 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7051 (ttm-80) REVERT: B 308 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7694 (ptp90) REVERT: B 314 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7188 (mtt) REVERT: B 474 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7663 (p0) REVERT: B 681 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8492 (p) REVERT: C 46 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7053 (ttm-80) REVERT: C 308 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7693 (ptp90) REVERT: C 314 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7188 (mtt) REVERT: C 474 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7661 (p0) REVERT: C 681 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8494 (p) REVERT: D 46 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7052 (ttm-80) REVERT: D 308 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7695 (ptp90) REVERT: D 314 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7187 (mtt) REVERT: D 474 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7667 (p0) REVERT: D 681 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8495 (p) outliers start: 150 outliers final: 114 residues processed: 416 average time/residue: 0.4688 time to fit residues: 323.3816 Evaluate side-chains 412 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 278 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1056 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 252 optimal weight: 6.9990 chunk 406 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 282 optimal weight: 0.9990 chunk 426 optimal weight: 9.9990 chunk 392 optimal weight: 0.9990 chunk 339 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 982 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 GLN B 982 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN C 775 GLN C 982 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 GLN D 982 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35376 Z= 0.192 Angle : 0.525 12.724 48020 Z= 0.275 Chirality : 0.043 0.163 5212 Planarity : 0.003 0.030 6216 Dihedral : 5.441 43.616 4636 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.73 % Allowed : 21.03 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.12), residues: 4296 helix: 1.14 (0.15), residues: 1188 sheet: -1.12 (0.15), residues: 964 loop : -2.13 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 159 HIS 0.004 0.001 HIS C 453 PHE 0.012 0.001 PHE B 856 TYR 0.024 0.001 TYR A 627 ARG 0.002 0.000 ARG C 677 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 288 time to evaluate : 4.045 Fit side-chains REVERT: A 46 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7047 (ttm-80) REVERT: A 308 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7694 (ptp90) REVERT: A 314 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7190 (mtt) REVERT: A 474 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7664 (p0) REVERT: A 681 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 46 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7049 (ttm-80) REVERT: B 308 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7695 (ptp90) REVERT: B 314 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7135 (mtt) REVERT: B 474 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7660 (p0) REVERT: B 681 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8505 (p) REVERT: C 46 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7049 (ttm-80) REVERT: C 308 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7694 (ptp90) REVERT: C 314 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7129 (mtt) REVERT: C 474 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7661 (p0) REVERT: C 681 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8503 (p) REVERT: D 46 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7051 (ttm-80) REVERT: D 308 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7694 (ptp90) REVERT: D 314 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7190 (mtt) REVERT: D 474 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7665 (p0) REVERT: D 681 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8504 (p) outliers start: 142 outliers final: 110 residues processed: 402 average time/residue: 0.4823 time to fit residues: 322.2527 Evaluate side-chains 418 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 288 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1056 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 269 optimal weight: 0.9990 chunk 361 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 313 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 340 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 349 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 GLN B 982 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 982 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 982 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098911 restraints weight = 50095.236| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.92 r_work: 0.3104 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35376 Z= 0.236 Angle : 0.539 12.844 48020 Z= 0.281 Chirality : 0.044 0.164 5212 Planarity : 0.003 0.032 6216 Dihedral : 5.481 43.552 4636 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.71 % Allowed : 21.32 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 4296 helix: 1.10 (0.15), residues: 1188 sheet: -1.14 (0.15), residues: 964 loop : -2.12 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 159 HIS 0.003 0.001 HIS C 453 PHE 0.014 0.001 PHE C 856 TYR 0.033 0.001 TYR D 627 ARG 0.002 0.000 ARG D 677 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7264.50 seconds wall clock time: 134 minutes 42.48 seconds (8082.48 seconds total)