Starting phenix.real_space_refine on Mon Jul 22 09:05:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/07_2024/8tnh_41416.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/07_2024/8tnh_41416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/07_2024/8tnh_41416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/07_2024/8tnh_41416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/07_2024/8tnh_41416.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/07_2024/8tnh_41416.cif" } resolution = 3.32 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 11001 2.51 5 N 2988 2.21 5 O 3555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 321": "OD1" <-> "OD2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E ASP 321": "OD1" <-> "OD2" Residue "E ASP 325": "OD1" <-> "OD2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17667 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "I" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.75, per 1000 atoms: 0.55 Number of scatterers: 17667 At special positions: 0 Unit cell: (136.53, 133.2, 126.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 3555 8.00 N 2988 7.00 C 11001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 50 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 197 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 197 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 197 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 262 " " NAG L 1 " - " ASN A 276 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 156 " " NAG R 1 " - " ASN C 160 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 363 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN E 156 " " NAG Z 1 " - " ASN E 262 " " NAG a 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 295 " " NAG c 1 " - " ASN E 332 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 386 " Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 3.3 seconds 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3926 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 44 sheets defined 19.8% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.106A pdb=" N GLU A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.685A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.969A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.465A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.863A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.721A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 664 removed outlier: 3.990A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 4.024A pdb=" N GLU C 62 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.683A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 4.004A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 335 through 349 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.096A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 597 removed outlier: 3.617A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.862A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR D 643 " --> pdb=" O THR D 639 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 removed outlier: 4.032A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.835A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.820A pdb=" N ASN E 98 " --> pdb=" O MET E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.714A pdb=" N GLN E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.628A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.783A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.838A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.728A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.929A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.635A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 641 through 664 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.676A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.667A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.729A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.666A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.290A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.432A pdb=" N CYS A 201 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 272 removed outlier: 7.871A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 272 removed outlier: 10.142A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 5.398A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.632A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.552A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.228A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.688A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.513A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 174 through 177 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 272 Processing sheet with id=AC1, first strand: chain 'C' and resid 377 through 378 removed outlier: 3.542A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 308 through 312 removed outlier: 6.807A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.744A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.410A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.214A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC9, first strand: chain 'E' and resid 173 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 161 through 162 removed outlier: 3.785A pdb=" N MET E 161 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 272 Processing sheet with id=AD3, first strand: chain 'E' and resid 416 through 417 removed outlier: 3.628A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AD5, first strand: chain 'E' and resid 308 through 312 removed outlier: 4.387A pdb=" N GLY E 312 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN E 315 " --> pdb=" O GLY E 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 393 through 395 removed outlier: 3.745A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 377 through 378 removed outlier: 3.540A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 423 through 424 removed outlier: 3.853A pdb=" N ILE E 424 " --> pdb=" O MET E 434 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG H 38 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR H 94 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR H 102 " --> pdb=" O THR H 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR I 94 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR I 102 " --> pdb=" O THR I 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.300A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.300A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR J 94 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1413 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: 6.01 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3272 1.33 - 1.46: 6720 1.46 - 1.60: 7837 1.60 - 1.74: 2 1.74 - 1.88: 160 Bond restraints: 17991 Sorted by residual: bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.331 1.365 -0.034 7.90e-03 1.60e+04 1.82e+01 bond pdb=" CA ALA A 319 " pdb=" CB ALA A 319 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.58e-02 4.01e+03 1.81e+01 bond pdb=" C TYR A 318 " pdb=" O TYR A 318 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.19e-02 7.06e+03 1.41e+01 bond pdb=" CA ALA C 319 " pdb=" CB ALA C 319 " ideal model delta sigma weight residual 1.535 1.462 0.072 1.93e-02 2.68e+03 1.41e+01 bond pdb=" C TYR E 318 " pdb=" O TYR E 318 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.26e-02 6.30e+03 9.81e+00 ... (remaining 17986 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.33: 411 106.33 - 113.26: 10280 113.26 - 120.20: 5845 120.20 - 127.14: 7673 127.14 - 134.08: 202 Bond angle restraints: 24411 Sorted by residual: angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 130.83 -16.43 2.30e+00 1.89e-01 5.10e+01 angle pdb=" C LYS C 155 " pdb=" N ASN C 156 " pdb=" CA ASN C 156 " ideal model delta sigma weight residual 122.93 114.23 8.70 1.45e+00 4.76e-01 3.60e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 127.28 -12.88 2.30e+00 1.89e-01 3.14e+01 angle pdb=" C ASN C 160 " pdb=" CA ASN C 160 " pdb=" CB ASN C 160 " ideal model delta sigma weight residual 111.70 118.28 -6.58 1.31e+00 5.83e-01 2.52e+01 angle pdb=" N CYS C 296 " pdb=" CA CYS C 296 " pdb=" C CYS C 296 " ideal model delta sigma weight residual 108.42 115.74 -7.32 1.54e+00 4.22e-01 2.26e+01 ... (remaining 24406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 10351 21.70 - 43.40: 1176 43.40 - 65.09: 237 65.09 - 86.79: 59 86.79 - 108.49: 18 Dihedral angle restraints: 11841 sinusoidal: 5754 harmonic: 6087 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -173.47 87.47 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -4.82 -81.18 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N MET C 161 " pdb=" CA MET C 161 " ideal model delta harmonic sigma weight residual -180.00 -142.88 -37.12 0 5.00e+00 4.00e-02 5.51e+01 ... (remaining 11838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 2947 0.238 - 0.476: 14 0.476 - 0.715: 0 0.715 - 0.953: 0 0.953 - 1.191: 1 Chirality restraints: 2962 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 156 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.55e+01 chirality pdb=" C1 NAG C 607 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG C 607 " pdb=" O5 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASP E 321A" pdb=" N ASP E 321A" pdb=" C ASP E 321A" pdb=" CB ASP E 321A" both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2959 not shown) Planarity restraints: 3091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 160 " 0.067 2.00e-02 2.50e+03 6.03e-02 4.55e+01 pdb=" CG ASN C 160 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN C 160 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 160 " -0.057 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.042 2.00e-02 2.50e+03 3.98e-02 1.98e+01 pdb=" CG ASN C 156 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " 0.038 2.00e-02 2.50e+03 3.59e-02 1.61e+01 pdb=" CG ASN A 339 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG A 608 " 0.040 2.00e-02 2.50e+03 ... (remaining 3088 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1246 2.73 - 3.27: 16167 3.27 - 3.82: 25524 3.82 - 4.36: 29141 4.36 - 4.90: 53977 Nonbonded interactions: 126055 Sorted by model distance: nonbonded pdb=" O SER C 375 " pdb=" OG SER C 375 " model vdw 2.191 2.440 nonbonded pdb=" NH2 ARG B 617 " pdb=" OE1 GLU B 634 " model vdw 2.199 2.520 nonbonded pdb=" OE1 GLN C 258 " pdb=" OG1 THR C 387 " model vdw 2.222 2.440 nonbonded pdb=" N GLU C 49 " pdb=" OE1 GLU C 49 " model vdw 2.244 2.520 nonbonded pdb=" O SER E 375 " pdb=" OG SER E 375 " model vdw 2.251 2.440 ... (remaining 126050 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' and (resid 31 through 505 or resid 601 through 607)) selection = chain 'C' selection = (chain 'E' and (resid 31 through 505 or resid 601 through 607)) } ncs_group { reference = (chain 'B' and resid 519 through 664) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'S' selection = chain 'Z' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 49.160 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 0.073 17991 Z= 0.309 Angle : 0.773 16.426 24411 Z= 0.404 Chirality : 0.057 1.191 2962 Planarity : 0.004 0.055 3042 Dihedral : 18.142 108.487 7798 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.05 % Favored : 90.71 % Rotamer: Outliers : 0.48 % Allowed : 32.14 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.36 (0.19), residues: 2077 helix: 1.96 (0.31), residues: 333 sheet: -0.75 (0.21), residues: 654 loop : -1.99 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 596 HIS 0.003 0.001 HIS J 100C PHE 0.023 0.001 PHE J 98 TYR 0.017 0.001 TYR C 484 ARG 0.007 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 335 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7559 (t0) cc_final: 0.7012 (t0) REVERT: B 588 ARG cc_start: 0.6581 (ttm110) cc_final: 0.6330 (ttm-80) REVERT: C 478 ASN cc_start: 0.8427 (m-40) cc_final: 0.8095 (t0) REVERT: H 79 TYR cc_start: 0.8715 (m-80) cc_final: 0.8140 (m-80) REVERT: H 95 ASP cc_start: 0.8524 (t0) cc_final: 0.8314 (m-30) REVERT: I 18 LEU cc_start: 0.8503 (mt) cc_final: 0.8202 (mp) REVERT: I 79 TYR cc_start: 0.8513 (m-80) cc_final: 0.8123 (m-80) REVERT: J 28 ASP cc_start: 0.8240 (p0) cc_final: 0.7389 (p0) REVERT: J 79 TYR cc_start: 0.8656 (m-80) cc_final: 0.8018 (m-80) outliers start: 9 outliers final: 2 residues processed: 342 average time/residue: 0.3431 time to fit residues: 167.7608 Evaluate side-chains 205 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain I residue 50 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 0.0670 overall best weight: 3.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 105 HIS A 289 ASN A 293 GLN A 330 HIS A 348 GLN B 651 ASN C 67 ASN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 293 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 348 GLN C 411 ASN D 625 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 411 ASN E 432 GLN F 590 GLN F 591 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN J 82BASN J 108 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17991 Z= 0.366 Angle : 0.730 13.367 24411 Z= 0.371 Chirality : 0.046 0.326 2962 Planarity : 0.004 0.041 3042 Dihedral : 10.478 73.680 3852 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.63 % Favored : 90.18 % Rotamer: Outliers : 6.17 % Allowed : 30.36 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 2077 helix: 2.00 (0.29), residues: 340 sheet: -0.85 (0.22), residues: 582 loop : -1.77 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 479 HIS 0.005 0.001 HIS J 100C PHE 0.019 0.001 PHE A 382 TYR 0.015 0.002 TYR H 60 ARG 0.007 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 216 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9303 (OUTLIER) cc_final: 0.8608 (m100) REVERT: A 114 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 185 ASN cc_start: 0.6935 (t0) cc_final: 0.6608 (t0) REVERT: E 161 MET cc_start: 0.7687 (tpp) cc_final: 0.7316 (tpt) REVERT: E 185 ASN cc_start: 0.6946 (t0) cc_final: 0.6720 (t0) REVERT: F 530 MET cc_start: 0.8410 (mmm) cc_final: 0.7964 (mpp) REVERT: I 79 TYR cc_start: 0.8177 (m-80) cc_final: 0.7842 (m-80) REVERT: I 82 MET cc_start: 0.8231 (mpp) cc_final: 0.7981 (mpp) REVERT: J 96 ARG cc_start: 0.8921 (mtp85) cc_final: 0.8694 (mtp85) outliers start: 115 outliers final: 53 residues processed: 318 average time/residue: 0.2918 time to fit residues: 139.1759 Evaluate side-chains 243 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 189 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN C 478 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 411 ASN E 440 GLN E 478 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 17991 Z= 0.448 Angle : 0.756 16.433 24411 Z= 0.385 Chirality : 0.046 0.254 2962 Planarity : 0.004 0.040 3042 Dihedral : 9.373 59.739 3851 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.16 % Favored : 89.70 % Rotamer: Outliers : 6.87 % Allowed : 31.06 % Favored : 62.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.24 (0.19), residues: 2077 helix: 2.11 (0.29), residues: 328 sheet: -0.85 (0.20), residues: 678 loop : -1.78 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 479 HIS 0.003 0.001 HIS J 100C PHE 0.016 0.002 PHE A 382 TYR 0.014 0.002 TYR E 61 ARG 0.009 0.001 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 202 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 278 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9258 (p) REVERT: C 185 ASN cc_start: 0.6892 (t0) cc_final: 0.6608 (t0) REVERT: E 185 ASN cc_start: 0.7141 (t0) cc_final: 0.6900 (t0) REVERT: H 82 MET cc_start: 0.8519 (mpp) cc_final: 0.8048 (mpp) REVERT: I 74 GLU cc_start: 0.8652 (pp20) cc_final: 0.8401 (pp20) REVERT: J 5 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8779 (tm-30) outliers start: 128 outliers final: 83 residues processed: 313 average time/residue: 0.2841 time to fit residues: 134.9762 Evaluate side-chains 267 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 183 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN E 478 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17991 Z= 0.230 Angle : 0.655 16.838 24411 Z= 0.338 Chirality : 0.045 0.239 2962 Planarity : 0.004 0.036 3042 Dihedral : 8.397 59.840 3851 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.57 % Favored : 91.33 % Rotamer: Outliers : 4.77 % Allowed : 33.32 % Favored : 61.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 2077 helix: 2.11 (0.30), residues: 328 sheet: -0.72 (0.21), residues: 654 loop : -1.69 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 479 HIS 0.004 0.001 HIS J 100C PHE 0.040 0.001 PHE F 519 TYR 0.016 0.001 TYR A 39 ARG 0.007 0.001 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 206 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8824 (tmm) cc_final: 0.8622 (tmm) REVERT: A 114 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8027 (tm-30) REVERT: C 185 ASN cc_start: 0.6867 (t0) cc_final: 0.6598 (t0) REVERT: E 185 ASN cc_start: 0.7083 (t0) cc_final: 0.6813 (t0) REVERT: H 5 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8586 (tm-30) REVERT: H 18 LEU cc_start: 0.9223 (tp) cc_final: 0.8869 (tp) REVERT: H 102 TYR cc_start: 0.8728 (m-80) cc_final: 0.8326 (m-10) REVERT: I 28 ASP cc_start: 0.8336 (p0) cc_final: 0.7834 (p0) REVERT: I 74 GLU cc_start: 0.8594 (pp20) cc_final: 0.8359 (pp20) REVERT: J 5 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8710 (tm-30) outliers start: 89 outliers final: 60 residues processed: 284 average time/residue: 0.2886 time to fit residues: 122.9795 Evaluate side-chains 245 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 185 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 17991 Z= 0.383 Angle : 0.717 15.773 24411 Z= 0.365 Chirality : 0.045 0.267 2962 Planarity : 0.004 0.046 3042 Dihedral : 8.017 58.695 3849 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.11 % Favored : 89.74 % Rotamer: Outliers : 6.44 % Allowed : 32.03 % Favored : 61.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.17 (0.19), residues: 2077 helix: 1.82 (0.29), residues: 342 sheet: -0.71 (0.21), residues: 645 loop : -1.70 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 479 HIS 0.003 0.001 HIS J 100C PHE 0.016 0.001 PHE A 382 TYR 0.024 0.002 TYR H 102 ARG 0.006 0.001 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 191 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9161 (p) REVERT: C 150 MET cc_start: 0.8759 (mpp) cc_final: 0.8521 (mpp) REVERT: C 185 ASN cc_start: 0.7015 (t0) cc_final: 0.6736 (t0) REVERT: E 150 MET cc_start: 0.8487 (mpp) cc_final: 0.8167 (mmm) REVERT: E 185 ASN cc_start: 0.7301 (t0) cc_final: 0.7051 (t0) REVERT: H 18 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8956 (tp) REVERT: I 82 MET cc_start: 0.8352 (mpp) cc_final: 0.8043 (mpp) REVERT: J 5 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8725 (tm-30) REVERT: J 28 ASP cc_start: 0.8806 (p0) cc_final: 0.8218 (p0) REVERT: J 30 GLU cc_start: 0.8107 (pm20) cc_final: 0.7855 (mp0) outliers start: 120 outliers final: 85 residues processed: 296 average time/residue: 0.2957 time to fit residues: 133.8750 Evaluate side-chains 265 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 178 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 82 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17991 Z= 0.249 Angle : 0.677 15.778 24411 Z= 0.345 Chirality : 0.045 0.239 2962 Planarity : 0.004 0.046 3042 Dihedral : 7.621 58.914 3849 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.91 % Favored : 90.95 % Rotamer: Outliers : 5.42 % Allowed : 32.73 % Favored : 61.86 % 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: -1.14 (0.19), residues: 2077 helix: 1.81 (0.29), residues: 342 sheet: -0.66 (0.21), residues: 657 loop : -1.71 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 427 HIS 0.003 0.001 HIS E 72 PHE 0.014 0.001 PHE A 382 TYR 0.017 0.001 TYR E 61 ARG 0.006 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 197 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9180 (p) REVERT: E 185 ASN cc_start: 0.7229 (t0) cc_final: 0.6966 (t0) REVERT: F 657 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8528 (pp20) REVERT: H 18 LEU cc_start: 0.9217 (tp) cc_final: 0.8939 (tp) REVERT: I 28 ASP cc_start: 0.8460 (p0) cc_final: 0.8004 (p0) REVERT: I 82 MET cc_start: 0.8316 (mpp) cc_final: 0.8057 (mpp) REVERT: J 5 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8701 (tm-30) REVERT: J 28 ASP cc_start: 0.8793 (p0) cc_final: 0.8175 (p0) REVERT: J 30 GLU cc_start: 0.8075 (pm20) cc_final: 0.7867 (mp0) outliers start: 101 outliers final: 77 residues processed: 287 average time/residue: 0.2896 time to fit residues: 126.9283 Evaluate side-chains 261 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 182 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 82 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 chunk 199 optimal weight: 0.0980 chunk 124 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17991 Z= 0.255 Angle : 0.683 15.340 24411 Z= 0.348 Chirality : 0.045 0.241 2962 Planarity : 0.004 0.052 3042 Dihedral : 7.347 58.515 3849 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.91 % Favored : 90.90 % Rotamer: Outliers : 5.15 % Allowed : 32.99 % Favored : 61.86 % 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: -1.19 (0.19), residues: 2077 helix: 1.69 (0.29), residues: 344 sheet: -0.69 (0.22), residues: 618 loop : -1.69 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 427 HIS 0.003 0.001 HIS J 100C PHE 0.025 0.001 PHE F 519 TYR 0.015 0.001 TYR E 61 ARG 0.006 0.000 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 193 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9123 (t0) cc_final: 0.8850 (p0) REVERT: C 104 MET cc_start: 0.8872 (ppp) cc_final: 0.8533 (tmm) REVERT: D 626 MET cc_start: 0.7777 (tpp) cc_final: 0.7007 (tpp) REVERT: E 185 ASN cc_start: 0.7244 (t0) cc_final: 0.6980 (t0) REVERT: F 657 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8494 (pp20) REVERT: H 18 LEU cc_start: 0.9215 (tp) cc_final: 0.8952 (tp) REVERT: I 82 MET cc_start: 0.8348 (mpp) cc_final: 0.8023 (mpp) REVERT: J 5 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8680 (tm-30) REVERT: J 28 ASP cc_start: 0.8733 (p0) cc_final: 0.8292 (p0) outliers start: 96 outliers final: 85 residues processed: 277 average time/residue: 0.2833 time to fit residues: 119.3041 Evaluate side-chains 266 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 180 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 82 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN E 33 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN J 82BASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 17991 Z= 0.335 Angle : 0.719 14.918 24411 Z= 0.366 Chirality : 0.045 0.238 2962 Planarity : 0.004 0.053 3042 Dihedral : 7.258 58.134 3849 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.92 % Favored : 89.89 % Rotamer: Outliers : 5.69 % Allowed : 32.35 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.19), residues: 2077 helix: 1.55 (0.29), residues: 344 sheet: -0.70 (0.22), residues: 618 loop : -1.70 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 479 HIS 0.003 0.001 HIS E 72 PHE 0.015 0.001 PHE A 382 TYR 0.015 0.001 TYR E 61 ARG 0.008 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 191 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9433 (OUTLIER) cc_final: 0.8469 (m100) REVERT: A 80 ASN cc_start: 0.9107 (t0) cc_final: 0.8844 (p0) REVERT: A 150 MET cc_start: 0.9202 (mpp) cc_final: 0.8500 (mmp) REVERT: E 185 ASN cc_start: 0.7295 (t0) cc_final: 0.7085 (t0) REVERT: H 18 LEU cc_start: 0.9237 (tp) cc_final: 0.8962 (tp) REVERT: I 28 ASP cc_start: 0.8481 (p0) cc_final: 0.8045 (p0) REVERT: I 82 MET cc_start: 0.8356 (mpp) cc_final: 0.8005 (mpp) REVERT: J 5 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8688 (tm-30) outliers start: 106 outliers final: 95 residues processed: 281 average time/residue: 0.2805 time to fit residues: 120.5585 Evaluate side-chains 277 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 181 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 82 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 122 optimal weight: 0.0470 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN H 3 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17991 Z= 0.215 Angle : 0.695 14.711 24411 Z= 0.354 Chirality : 0.045 0.248 2962 Planarity : 0.004 0.063 3042 Dihedral : 6.949 58.385 3849 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.38 % Favored : 91.48 % Rotamer: Outliers : 4.40 % Allowed : 33.58 % Favored : 62.02 % 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: -1.06 (0.19), residues: 2077 helix: 1.62 (0.29), residues: 343 sheet: -0.52 (0.22), residues: 588 loop : -1.58 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 479 HIS 0.003 0.001 HIS J 100C PHE 0.013 0.001 PHE A 382 TYR 0.015 0.001 TYR A 61 ARG 0.015 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 196 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9407 (OUTLIER) cc_final: 0.8449 (m100) REVERT: A 80 ASN cc_start: 0.9042 (t0) cc_final: 0.8747 (p0) REVERT: C 95 MET cc_start: 0.8992 (ppp) cc_final: 0.8288 (ppp) REVERT: C 150 MET cc_start: 0.8815 (mpp) cc_final: 0.8575 (mpp) REVERT: E 185 ASN cc_start: 0.7208 (t0) cc_final: 0.6991 (t0) REVERT: H 18 LEU cc_start: 0.9194 (tp) cc_final: 0.8927 (tp) REVERT: I 28 ASP cc_start: 0.8356 (p0) cc_final: 0.7935 (p0) REVERT: I 82 MET cc_start: 0.8322 (mpp) cc_final: 0.7949 (mpp) REVERT: J 5 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8659 (tm-30) REVERT: J 28 ASP cc_start: 0.8781 (p0) cc_final: 0.8576 (p0) outliers start: 82 outliers final: 71 residues processed: 265 average time/residue: 0.2909 time to fit residues: 117.0218 Evaluate side-chains 254 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 182 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 17991 Z= 0.356 Angle : 0.748 14.252 24411 Z= 0.382 Chirality : 0.045 0.238 2962 Planarity : 0.004 0.059 3042 Dihedral : 6.979 57.887 3849 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.26 % Favored : 89.55 % Rotamer: Outliers : 4.24 % Allowed : 33.96 % Favored : 61.80 % 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: -1.13 (0.19), residues: 2077 helix: 1.60 (0.30), residues: 341 sheet: -0.59 (0.21), residues: 648 loop : -1.65 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 479 HIS 0.003 0.001 HIS E 72 PHE 0.030 0.001 PHE F 519 TYR 0.014 0.001 TYR H 79 ARG 0.008 0.000 ARG J 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 189 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9101 (t0) cc_final: 0.8746 (p0) REVERT: E 185 ASN cc_start: 0.7350 (t0) cc_final: 0.7150 (t0) REVERT: H 18 LEU cc_start: 0.9253 (tp) cc_final: 0.8968 (tp) REVERT: H 44 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7663 (tm-30) REVERT: I 74 GLU cc_start: 0.8726 (pp20) cc_final: 0.8512 (pp20) REVERT: I 82 MET cc_start: 0.8369 (mpp) cc_final: 0.7976 (mpp) REVERT: J 5 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8693 (tm-30) REVERT: J 28 ASP cc_start: 0.8990 (p0) cc_final: 0.8518 (p0) REVERT: J 92 CYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5908 (p) outliers start: 79 outliers final: 74 residues processed: 258 average time/residue: 0.2864 time to fit residues: 112.5887 Evaluate side-chains 254 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 179 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.048156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.035650 restraints weight = 85963.568| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 6.19 r_work: 0.2405 rms_B_bonded: 6.18 restraints_weight: 2.0000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17991 Z= 0.212 Angle : 0.717 14.209 24411 Z= 0.365 Chirality : 0.046 0.253 2962 Planarity : 0.004 0.049 3042 Dihedral : 6.707 58.586 3849 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.18 % Favored : 91.67 % Rotamer: Outliers : 3.70 % Allowed : 34.39 % Favored : 61.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 2077 helix: 1.48 (0.30), residues: 343 sheet: -0.48 (0.22), residues: 588 loop : -1.54 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 479 HIS 0.005 0.001 HIS J 100C PHE 0.013 0.001 PHE A 382 TYR 0.017 0.001 TYR B 638 ARG 0.009 0.001 ARG D 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3723.96 seconds wall clock time: 67 minutes 33.41 seconds (4053.41 seconds total)