Starting phenix.real_space_refine on Wed Apr 10 18:44:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/04_2024/8sb5_40291_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/04_2024/8sb5_40291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/04_2024/8sb5_40291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/04_2024/8sb5_40291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/04_2024/8sb5_40291_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/04_2024/8sb5_40291_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 141 5.16 5 C 12620 2.51 5 N 3338 2.21 5 O 4106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 457": "OD1" <-> "OD2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 624": "OD1" <-> "OD2" Residue "G ASP 632": "OD1" <-> "OD2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 115": "OD1" <-> "OD2" Residue "I TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 314": "OD1" <-> "OD2" Residue "K ASP 57": "OD1" <-> "OD2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 466": "OE1" <-> "OE2" Residue "K TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 589": "OD1" <-> "OD2" Residue "L ASP 624": "OD1" <-> "OD2" Residue "L TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 654": "OE1" <-> "OE2" Residue "M PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 115": "OD1" <-> "OD2" Residue "N TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 314": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20205 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3607 Classifications: {'peptide': 461} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "H" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "M" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" 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: "J" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" 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: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" 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: "U" 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: "V" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" 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 Time building chain proxies: 10.89, per 1000 atoms: 0.54 Number of scatterers: 20205 At special positions: 0 Unit cell: (156, 154.96, 134.16, 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 141 16.00 O 4106 8.00 N 3338 7.00 C 12620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 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 A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 321 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS I 320 " distance=2.03 Simple disulfide: pdb=" SG CYS I 321 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.04 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 252 " - pdb=" SG CYS N 320 " distance=2.03 Simple disulfide: pdb=" SG CYS N 321 " - pdb=" SG CYS N 331 " 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 ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN J 10 " - " MAN J 11 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " " MAN V 10 " - " MAN V 11 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 10 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 10 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 8.85 Conformation dependent library (CDL) restraints added in 3.4 seconds 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 46 sheets defined 20.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.472A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.957A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.494A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.562A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.285A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.760A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 311 through 315 removed outlier: 3.700A pdb=" N GLU D 315 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.472A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.674A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 4.453A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 596 Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.359A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 3.744A pdb=" N ILE G 642 " --> pdb=" O TYR G 638 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU G 647 " --> pdb=" O TYR G 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 311 through 315 Processing helix chain 'K' and resid 57 through 61 Processing helix chain 'K' and resid 68 through 72 Processing helix chain 'K' and resid 98 through 117 removed outlier: 4.522A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 387 through 390 Processing helix chain 'K' and resid 475 through 481 removed outlier: 3.712A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 534 Processing helix chain 'L' and resid 536 through 543 removed outlier: 4.471A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.542A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.313A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 3.768A pdb=" N ILE L 642 " --> pdb=" O TYR L 638 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU L 647 " --> pdb=" O TYR L 643 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 311 through 315 removed outlier: 3.615A pdb=" N GLU N 315 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.599A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 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 169 through 176 removed outlier: 4.312A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.746A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.234A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.185A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.234A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 308 removed outlier: 5.450A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.505A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.811A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP C 50 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 93 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 98 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS C 116 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.811A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP C 50 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 93 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 253 Processing sheet with id=AB5, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.438A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR D 281 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 265 " --> pdb=" O TYR D 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.438A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR D 281 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 265 " --> pdb=" O TYR D 281 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 499 Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.241A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.751A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS F 218 " --> pdb=" O PHE F 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 176 removed outlier: 4.581A pdb=" N ASN F 156 " --> pdb=" O SER F 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.775A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.306A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.186A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.306A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 359 " --> pdb=" O TYR F 395 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.457A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.735A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL H 93 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS H 116 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.735A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL H 93 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 248 through 253 Processing sheet with id=AD2, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.478A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR I 281 " --> pdb=" O VAL I 265 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 265 " --> pdb=" O TYR I 281 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.478A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR I 281 " --> pdb=" O VAL I 265 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 265 " --> pdb=" O TYR I 281 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 494 through 499 Processing sheet with id=AD5, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.590A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU K 84 " --> pdb=" O THR K 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 55 through 56 Processing sheet with id=AD7, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'K' and resid 169 through 176 removed outlier: 4.361A pdb=" N ASN K 156 " --> pdb=" O SER K 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 259 through 261 removed outlier: 3.787A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.926A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.215A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 259 through 261 removed outlier: 3.787A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.926A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.215A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 302 through 308 removed outlier: 5.409A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 394 through 395 removed outlier: 3.623A pdb=" N ILE K 359 " --> pdb=" O TYR K 395 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.905A pdb=" N ASN M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP M 50 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL M 93 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS M 116 " --> pdb=" O THR M 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.905A pdb=" N ASN M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP M 50 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL M 93 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 248 through 253 Processing sheet with id=AE9, first strand: chain 'N' and resid 277 through 281 removed outlier: 6.593A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 277 through 281 removed outlier: 6.593A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 9.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4671 1.33 - 1.45: 4828 1.45 - 1.58: 10932 1.58 - 1.70: 10 1.70 - 1.82: 192 Bond restraints: 20633 Sorted by residual: bond pdb=" C1 BMA X 3 " pdb=" C2 BMA X 3 " ideal model delta sigma weight residual 1.519 1.607 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 BMA T 3 " pdb=" C2 BMA T 3 " ideal model delta sigma weight residual 1.519 1.604 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.601 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 MAN V 9 " pdb=" C2 MAN V 9 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.472 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 20628 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.47: 596 106.47 - 113.64: 11815 113.64 - 120.80: 8200 120.80 - 127.96: 7166 127.96 - 135.12: 287 Bond angle restraints: 28064 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.70 -11.00 1.80e+00 3.09e-01 3.73e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 132.61 -10.91 1.80e+00 3.09e-01 3.67e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.60 -10.90 1.80e+00 3.09e-01 3.67e+01 angle pdb=" C ASN F 403 " pdb=" N SER F 404 " pdb=" CA SER F 404 " ideal model delta sigma weight residual 121.70 130.99 -9.29 1.80e+00 3.09e-01 2.66e+01 angle pdb=" C ASN K 403 " pdb=" N SER K 404 " pdb=" CA SER K 404 " ideal model delta sigma weight residual 121.70 130.87 -9.17 1.80e+00 3.09e-01 2.60e+01 ... (remaining 28059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 12348 22.74 - 45.48: 661 45.48 - 68.22: 89 68.22 - 90.96: 99 90.96 - 113.69: 48 Dihedral angle restraints: 13245 sinusoidal: 6091 harmonic: 7154 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -149.71 63.71 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS K 119 " pdb=" SG CYS K 119 " pdb=" SG CYS K 205 " pdb=" CB CYS K 205 " ideal model delta sinusoidal sigma weight residual -86.00 -148.18 62.18 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -146.87 60.87 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 13242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2785 0.066 - 0.131: 492 0.131 - 0.197: 83 0.197 - 0.262: 3 0.262 - 0.328: 11 Chirality restraints: 3374 Sorted by residual: chirality pdb=" CA THR A 123 " pdb=" N THR A 123 " pdb=" C THR A 123 " pdb=" CB THR A 123 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3371 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 84 " -0.364 9.50e-02 1.11e+02 1.63e-01 1.78e+01 pdb=" NE ARG M 84 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG M 84 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG M 84 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG M 84 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 596 " 0.028 2.00e-02 2.50e+03 1.91e-02 9.16e+00 pdb=" CG TRP L 596 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP L 596 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP L 596 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP L 596 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 596 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP L 596 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 596 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 596 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 596 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 596 " 0.024 2.00e-02 2.50e+03 1.69e-02 7.12e+00 pdb=" CG TRP B 596 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 596 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 596 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 596 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 596 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 596 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 596 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 596 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 596 " 0.001 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 386 2.66 - 3.22: 19495 3.22 - 3.78: 29478 3.78 - 4.34: 41440 4.34 - 4.90: 69021 Nonbonded interactions: 159820 Sorted by model distance: nonbonded pdb=" OG1 THR M 28 " pdb=" OD2 ASP M 31 " model vdw 2.103 2.440 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.124 2.440 nonbonded pdb=" OD1 ASN K 463 " pdb=" OG1 THR K 465 " model vdw 2.136 2.440 nonbonded pdb=" OG1 THR G 529 " pdb=" O ASP G 624 " model vdw 2.143 2.440 nonbonded pdb=" OG SER I 295 " pdb=" OG1 THR I 306 " model vdw 2.160 2.440 ... (remaining 159815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'F' and (resid 32 through 443 or resid 445 through 505)) selection = (chain 'K' and (resid 32 through 443 or resid 445 through 505)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.080 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 54.550 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 : 0.006 0.114 20633 Z= 0.389 Angle : 0.996 10.998 28064 Z= 0.508 Chirality : 0.055 0.328 3374 Planarity : 0.006 0.163 3469 Dihedral : 17.058 113.694 8534 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.20 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2463 helix: -0.60 (0.26), residues: 399 sheet: -0.72 (0.20), residues: 614 loop : -1.24 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP L 596 HIS 0.012 0.002 HIS A 374 PHE 0.010 0.001 PHE A 376 TYR 0.032 0.003 TYR K 395 ARG 0.021 0.001 ARG M 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.197 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: A 423 ILE cc_start: 0.8929 (mm) cc_final: 0.8615 (mm) REVERT: B 535 MET cc_start: 0.7560 (mmm) cc_final: 0.7321 (mmt) REVERT: D 271 HIS cc_start: 0.6171 (m-70) cc_final: 0.5957 (m-70) REVERT: H 27 TYR cc_start: 0.4325 (m-10) cc_final: 0.3870 (m-80) REVERT: M 6 GLN cc_start: 0.7203 (mt0) cc_final: 0.6878 (mt0) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.3233 time to fit residues: 185.1401 Evaluate side-chains 287 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 289 HIS A 374 HIS C 43 GLN F 229 ASN F 289 HIS F 374 HIS G 577 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 229 ASN ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS K 374 HIS M 43 GLN N 270 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20633 Z= 0.355 Angle : 0.809 13.876 28064 Z= 0.409 Chirality : 0.050 0.206 3374 Planarity : 0.005 0.057 3469 Dihedral : 13.283 87.731 4119 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 1.54 % Allowed : 8.44 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.32 (0.17), residues: 2463 helix: 0.15 (0.27), residues: 372 sheet: -0.78 (0.19), residues: 655 loop : -1.19 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.009 0.002 HIS C 35 PHE 0.025 0.003 PHE A 391 TYR 0.027 0.003 TYR D 281 ARG 0.033 0.001 ARG L 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 294 time to evaluate : 2.184 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: A 112 TRP cc_start: 0.7006 (m-90) cc_final: 0.6644 (t-100) REVERT: A 374 HIS cc_start: 0.9081 (OUTLIER) cc_final: 0.8773 (t70) REVERT: A 395 TYR cc_start: 0.6419 (t80) cc_final: 0.5976 (t80) REVERT: A 423 ILE cc_start: 0.9248 (mm) cc_final: 0.9010 (mt) REVERT: B 542 ARG cc_start: 0.7352 (ttm170) cc_final: 0.6826 (ttm170) REVERT: F 45 TRP cc_start: 0.8048 (m-10) cc_final: 0.7828 (m-10) REVERT: F 374 HIS cc_start: 0.9235 (OUTLIER) cc_final: 0.8827 (t-170) REVERT: K 374 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8663 (t70) REVERT: M 81 MET cc_start: 0.7641 (tmm) cc_final: 0.7416 (tmm) outliers start: 33 outliers final: 20 residues processed: 316 average time/residue: 0.3143 time to fit residues: 153.3006 Evaluate side-chains 279 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 651 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 HIS ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20633 Z= 0.263 Angle : 0.717 12.995 28064 Z= 0.366 Chirality : 0.046 0.202 3374 Planarity : 0.004 0.059 3469 Dihedral : 11.784 85.630 4119 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.93 % Favored : 93.75 % Rotamer: Outliers : 2.33 % Allowed : 10.87 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2463 helix: 0.29 (0.27), residues: 378 sheet: -0.64 (0.20), residues: 642 loop : -1.12 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 35 HIS 0.006 0.001 HIS H 35 PHE 0.016 0.002 PHE K 391 TYR 0.025 0.002 TYR N 319 ARG 0.013 0.000 ARG G 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 267 time to evaluate : 1.894 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: A 475 MET cc_start: 0.6138 (mmt) cc_final: 0.5873 (tpt) REVERT: B 542 ARG cc_start: 0.7367 (ttm170) cc_final: 0.5986 (ttm170) REVERT: F 434 MET cc_start: 0.8535 (ttp) cc_final: 0.8038 (ttp) REVERT: I 305 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6239 (tp) REVERT: K 112 TRP cc_start: 0.7416 (t-100) cc_final: 0.6740 (t-100) REVERT: M 81 MET cc_start: 0.7569 (tmm) cc_final: 0.7235 (tmm) outliers start: 50 outliers final: 28 residues processed: 304 average time/residue: 0.3089 time to fit residues: 146.4601 Evaluate side-chains 281 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 252 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain N residue 320 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 241 ASN A 289 HIS A 422 GLN F 229 ASN F 241 ASN F 352 HIS F 374 HIS F 422 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 229 ASN K 241 ASN ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN N 311 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20633 Z= 0.390 Angle : 0.783 14.743 28064 Z= 0.396 Chirality : 0.048 0.246 3374 Planarity : 0.005 0.058 3469 Dihedral : 11.034 87.741 4119 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.63 % Favored : 92.04 % Rotamer: Outliers : 3.08 % Allowed : 12.69 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -1.29 (0.16), residues: 2463 helix: 0.23 (0.27), residues: 390 sheet: -0.73 (0.20), residues: 637 loop : -1.23 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 571 HIS 0.010 0.002 HIS A 289 PHE 0.022 0.002 PHE I 323 TYR 0.022 0.002 TYR D 281 ARG 0.008 0.001 ARG G 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 266 time to evaluate : 2.141 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: A 395 TYR cc_start: 0.6254 (t80) cc_final: 0.5828 (t80) REVERT: A 423 ILE cc_start: 0.9134 (mt) cc_final: 0.8842 (mt) REVERT: B 520 LEU cc_start: 0.6094 (mt) cc_final: 0.5833 (mp) REVERT: B 542 ARG cc_start: 0.7412 (ttm170) cc_final: 0.6569 (ttm170) REVERT: F 374 HIS cc_start: 0.9248 (OUTLIER) cc_final: 0.8829 (t70) REVERT: F 481 SER cc_start: 0.9361 (p) cc_final: 0.9124 (t) REVERT: I 305 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6255 (tp) REVERT: K 112 TRP cc_start: 0.7467 (t-100) cc_final: 0.6811 (t-100) REVERT: K 374 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8806 (t-170) REVERT: K 481 SER cc_start: 0.9321 (p) cc_final: 0.9062 (t) outliers start: 66 outliers final: 42 residues processed: 322 average time/residue: 0.3083 time to fit residues: 156.6863 Evaluate side-chains 289 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 244 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain N residue 269 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 213 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20633 Z= 0.223 Angle : 0.690 13.005 28064 Z= 0.351 Chirality : 0.045 0.203 3374 Planarity : 0.004 0.056 3469 Dihedral : 9.920 80.162 4119 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.17 % Favored : 93.50 % Rotamer: Outliers : 2.38 % Allowed : 14.51 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.01 (0.17), residues: 2463 helix: 0.67 (0.27), residues: 381 sheet: -0.51 (0.20), residues: 629 loop : -1.11 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 571 HIS 0.018 0.001 HIS F 374 PHE 0.016 0.001 PHE A 210 TYR 0.031 0.002 TYR F 486 ARG 0.004 0.000 ARG L 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 262 time to evaluate : 2.132 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: B 542 ARG cc_start: 0.7426 (ttm170) cc_final: 0.6678 (ttm170) REVERT: F 112 TRP cc_start: 0.7496 (t-100) cc_final: 0.7141 (t-100) REVERT: F 374 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8235 (t-170) REVERT: F 481 SER cc_start: 0.9317 (p) cc_final: 0.9117 (t) REVERT: I 305 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6072 (tp) REVERT: K 112 TRP cc_start: 0.7272 (t-100) cc_final: 0.6704 (t-100) REVERT: K 481 SER cc_start: 0.9282 (p) cc_final: 0.9039 (t) outliers start: 51 outliers final: 35 residues processed: 302 average time/residue: 0.3079 time to fit residues: 146.5172 Evaluate side-chains 283 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 246 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain N residue 269 GLN Chi-restraints excluded: chain N residue 320 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 197 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20633 Z= 0.297 Angle : 0.710 12.857 28064 Z= 0.360 Chirality : 0.046 0.207 3374 Planarity : 0.004 0.056 3469 Dihedral : 9.859 80.835 4119 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.11 % Favored : 92.57 % Rotamer: Outliers : 3.26 % Allowed : 14.74 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.00 (0.17), residues: 2463 helix: 0.73 (0.27), residues: 381 sheet: -0.58 (0.20), residues: 637 loop : -1.08 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 571 HIS 0.007 0.001 HIS H 35 PHE 0.014 0.002 PHE D 323 TYR 0.027 0.002 TYR F 486 ARG 0.004 0.000 ARG K 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 247 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: A 298 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8396 (mtm110) REVERT: B 542 ARG cc_start: 0.7426 (ttm170) cc_final: 0.6593 (ttm170) REVERT: F 112 TRP cc_start: 0.7640 (t-100) cc_final: 0.7290 (t-100) REVERT: F 374 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8369 (t-170) REVERT: F 481 SER cc_start: 0.9371 (p) cc_final: 0.9162 (t) REVERT: H 47 TRP cc_start: 0.8050 (t60) cc_final: 0.7641 (t60) REVERT: I 305 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6079 (tp) REVERT: K 112 TRP cc_start: 0.7319 (t-100) cc_final: 0.6735 (t-100) REVERT: K 374 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8398 (t-90) outliers start: 70 outliers final: 50 residues processed: 305 average time/residue: 0.3222 time to fit residues: 152.4142 Evaluate side-chains 295 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 241 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain N residue 269 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 134 optimal weight: 0.0030 chunk 200 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 237 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN N 271 HIS N 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20633 Z= 0.193 Angle : 0.658 12.987 28064 Z= 0.335 Chirality : 0.045 0.207 3374 Planarity : 0.004 0.055 3469 Dihedral : 9.177 74.648 4119 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.81 % Favored : 93.87 % Rotamer: Outliers : 3.12 % Allowed : 15.11 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2463 helix: 0.95 (0.27), residues: 381 sheet: -0.26 (0.20), residues: 611 loop : -1.02 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 571 HIS 0.018 0.001 HIS F 374 PHE 0.010 0.001 PHE K 376 TYR 0.021 0.002 TYR F 486 ARG 0.003 0.000 ARG L 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 273 time to evaluate : 2.161 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: A 180 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8107 (t0) REVERT: A 298 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8354 (mtm110) REVERT: A 417 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8267 (mm-40) REVERT: B 542 ARG cc_start: 0.7439 (ttm170) cc_final: 0.6622 (ttm170) REVERT: C 47 TRP cc_start: 0.8241 (t60) cc_final: 0.7967 (t60) REVERT: F 112 TRP cc_start: 0.7483 (t-100) cc_final: 0.7181 (t-100) REVERT: F 298 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8433 (ttp-170) REVERT: F 374 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8080 (t-170) REVERT: F 377 ASN cc_start: 0.8569 (t0) cc_final: 0.8367 (t0) REVERT: F 481 SER cc_start: 0.9341 (p) cc_final: 0.9138 (t) REVERT: H 47 TRP cc_start: 0.8158 (t60) cc_final: 0.7513 (t60) REVERT: I 293 ARG cc_start: 0.7547 (mtp180) cc_final: 0.7327 (mtp180) REVERT: I 305 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5978 (tp) REVERT: K 112 TRP cc_start: 0.7168 (t-100) cc_final: 0.6674 (t-100) REVERT: K 374 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8351 (t-90) REVERT: M 47 TRP cc_start: 0.8186 (t60) cc_final: 0.7464 (t60) outliers start: 67 outliers final: 43 residues processed: 325 average time/residue: 0.3483 time to fit residues: 178.4457 Evaluate side-chains 309 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 259 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS D 270 GLN F 374 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20633 Z= 0.246 Angle : 0.679 12.300 28064 Z= 0.345 Chirality : 0.045 0.223 3374 Planarity : 0.004 0.053 3469 Dihedral : 9.088 74.743 4119 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.74 % Favored : 92.98 % Rotamer: Outliers : 3.08 % Allowed : 16.00 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2463 helix: 0.99 (0.28), residues: 381 sheet: -0.18 (0.21), residues: 605 loop : -1.01 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 596 HIS 0.009 0.001 HIS F 374 PHE 0.013 0.001 PHE K 376 TYR 0.021 0.002 TYR N 281 ARG 0.003 0.000 ARG L 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 263 time to evaluate : 2.264 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: A 180 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8050 (t0) REVERT: A 298 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8345 (mtm110) REVERT: A 417 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8238 (mm-40) REVERT: B 542 ARG cc_start: 0.7465 (ttm170) cc_final: 0.6615 (ttm170) REVERT: C 47 TRP cc_start: 0.8268 (t60) cc_final: 0.8027 (t60) REVERT: F 112 TRP cc_start: 0.7451 (t-100) cc_final: 0.7131 (t-100) REVERT: F 374 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.7589 (t-170) REVERT: F 377 ASN cc_start: 0.8591 (t0) cc_final: 0.8358 (t0) REVERT: F 481 SER cc_start: 0.9377 (p) cc_final: 0.9131 (t) REVERT: G 602 LEU cc_start: 0.7779 (pt) cc_final: 0.7467 (mp) REVERT: H 47 TRP cc_start: 0.8146 (t60) cc_final: 0.7552 (t60) REVERT: I 305 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5944 (tp) REVERT: K 112 TRP cc_start: 0.7204 (t-100) cc_final: 0.6669 (t-100) REVERT: K 374 HIS cc_start: 0.8924 (OUTLIER) cc_final: 0.8473 (t-170) REVERT: M 47 TRP cc_start: 0.8233 (t60) cc_final: 0.7481 (t60) outliers start: 66 outliers final: 51 residues processed: 315 average time/residue: 0.3122 time to fit residues: 153.7062 Evaluate side-chains 313 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 256 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 199 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN F 374 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20633 Z= 0.203 Angle : 0.651 11.987 28064 Z= 0.332 Chirality : 0.045 0.185 3374 Planarity : 0.004 0.052 3469 Dihedral : 8.705 71.573 4119 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.97 % Favored : 93.79 % Rotamer: Outliers : 3.03 % Allowed : 16.18 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2463 helix: 1.09 (0.28), residues: 381 sheet: -0.11 (0.21), residues: 611 loop : -0.97 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 596 HIS 0.022 0.001 HIS F 374 PHE 0.013 0.001 PHE K 376 TYR 0.022 0.002 TYR N 281 ARG 0.003 0.000 ARG L 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 269 time to evaluate : 1.959 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 180 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8031 (t0) REVERT: A 298 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8343 (mtm180) REVERT: A 417 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8169 (mm-40) REVERT: B 542 ARG cc_start: 0.7485 (ttm170) cc_final: 0.6666 (ttm170) REVERT: F 84 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6250 (tt) REVERT: F 112 TRP cc_start: 0.7394 (t-100) cc_final: 0.7017 (t-100) REVERT: F 374 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8203 (t70) REVERT: F 481 SER cc_start: 0.9370 (p) cc_final: 0.9117 (t) REVERT: G 542 ARG cc_start: 0.7437 (ttm170) cc_final: 0.6798 (ttm170) REVERT: H 47 TRP cc_start: 0.8231 (t60) cc_final: 0.7028 (t60) REVERT: I 305 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5848 (tp) REVERT: K 112 TRP cc_start: 0.7182 (t-100) cc_final: 0.6645 (t-100) REVERT: K 374 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8509 (t-170) REVERT: M 47 TRP cc_start: 0.8211 (t60) cc_final: 0.7704 (t60) outliers start: 65 outliers final: 48 residues processed: 320 average time/residue: 0.3166 time to fit residues: 158.2036 Evaluate side-chains 320 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 265 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain N residue 263 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 374 HIS ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20633 Z= 0.381 Angle : 0.750 12.282 28064 Z= 0.381 Chirality : 0.048 0.195 3374 Planarity : 0.005 0.053 3469 Dihedral : 9.294 77.265 4119 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.20 % Favored : 91.56 % Rotamer: Outliers : 2.99 % Allowed : 16.56 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2463 helix: 0.64 (0.27), residues: 399 sheet: -0.47 (0.20), residues: 637 loop : -1.02 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP L 596 HIS 0.025 0.002 HIS F 374 PHE 0.021 0.002 PHE I 323 TYR 0.026 0.002 TYR N 281 ARG 0.006 0.001 ARG K 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 270 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8224 (t0) REVERT: A 374 HIS cc_start: 0.9194 (OUTLIER) cc_final: 0.8775 (t-170) REVERT: A 395 TYR cc_start: 0.6246 (t80) cc_final: 0.5990 (t80) REVERT: A 417 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8082 (mm-40) REVERT: A 426 MET cc_start: 0.7005 (mtm) cc_final: 0.6225 (mtm) REVERT: A 475 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6119 (tpp) REVERT: B 542 ARG cc_start: 0.7513 (ttm170) cc_final: 0.6541 (ttm170) REVERT: D 270 GLN cc_start: 0.7875 (pm20) cc_final: 0.7612 (pm20) REVERT: F 84 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6371 (tt) REVERT: F 112 TRP cc_start: 0.7438 (t-100) cc_final: 0.7082 (t-100) REVERT: F 374 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.8570 (t-170) REVERT: H 47 TRP cc_start: 0.8191 (t60) cc_final: 0.7532 (t60) REVERT: I 293 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7371 (mtp180) REVERT: I 305 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5939 (tp) REVERT: K 99 ASP cc_start: 0.8328 (p0) cc_final: 0.8093 (p0) REVERT: K 112 TRP cc_start: 0.7294 (t-100) cc_final: 0.6830 (t-100) REVERT: K 374 HIS cc_start: 0.9034 (OUTLIER) cc_final: 0.8466 (t-170) REVERT: M 11 MET cc_start: 0.4599 (ttt) cc_final: 0.4251 (ttt) outliers start: 64 outliers final: 50 residues processed: 322 average time/residue: 0.3112 time to fit residues: 156.1829 Evaluate side-chains 317 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 259 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain N residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 171 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS ** F 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 GLN ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.165770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150646 restraints weight = 28251.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145603 restraints weight = 40640.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144917 restraints weight = 31823.836| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20633 Z= 0.197 Angle : 0.663 11.732 28064 Z= 0.339 Chirality : 0.045 0.185 3374 Planarity : 0.004 0.051 3469 Dihedral : 8.567 70.895 4119 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.97 % Favored : 93.79 % Rotamer: Outliers : 2.61 % Allowed : 17.26 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2463 helix: 0.96 (0.28), residues: 387 sheet: -0.19 (0.21), residues: 568 loop : -0.99 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 596 HIS 0.010 0.001 HIS A 374 PHE 0.013 0.001 PHE K 376 TYR 0.023 0.002 TYR I 281 ARG 0.003 0.000 ARG B 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4091.08 seconds wall clock time: 76 minutes 34.28 seconds (4594.28 seconds total)