Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 20:12:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/05_2023/8sb5_40291_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/05_2023/8sb5_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_40291/05_2023/8sb5_40291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/05_2023/8sb5_40291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/05_2023/8sb5_40291_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb5_40291/05_2023/8sb5_40291_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 10.42, per 1000 atoms: 0.52 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: 9.18 Conformation dependent library (CDL) restraints added in 2.9 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: 1.39 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: 7.47 Time building geometry restraints manager: 9.85 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 - 17.96: 10716 17.96 - 35.92: 841 35.92 - 53.88: 182 53.88 - 71.84: 32 71.84 - 89.81: 20 Dihedral angle restraints: 11791 sinusoidal: 4637 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 11788 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: 2.450 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: 8.900 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 52.680 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.770 ------------------------------------------------------------------------------- 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 : 13.776 89.806 7080 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 % 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 *********************** 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 : 2.486 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 outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.3131 time to fit residues: 179.1978 Evaluate side-chains 285 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0327 ------------------------------------------------------------------------------- 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: 0.5980 chunk 117 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 A 422 GLN C 43 GLN D 271 HIS F 229 ASN F 289 HIS F 374 HIS G 577 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 20633 Z= 0.392 Angle : 0.822 14.088 28064 Z= 0.418 Chirality : 0.049 0.205 3374 Planarity : 0.005 0.059 3469 Dihedral : 6.728 32.033 2665 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.46 % Favored : 93.22 % Rotamer Outliers : 1.45 % 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: -1.40 (0.16), residues: 2463 helix: 0.01 (0.27), residues: 378 sheet: -0.81 (0.19), residues: 654 loop : -1.23 (0.16), residues: 1431 *********************** 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 317 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 286 time to evaluate : 2.255 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 outliers start: 31 outliers final: 18 residues processed: 306 average time/residue: 0.3200 time to fit residues: 150.7491 Evaluate side-chains 275 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 257 time to evaluate : 2.066 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1846 time to fit residues: 9.4772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.0030 chunk 69 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN F 374 HIS ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 20633 Z= 0.264 Angle : 0.713 13.044 28064 Z= 0.365 Chirality : 0.046 0.194 3374 Planarity : 0.005 0.059 3469 Dihedral : 6.320 31.770 2665 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.01 % Favored : 93.67 % Rotamer Outliers : 1.91 % 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: -1.16 (0.17), residues: 2463 helix: 0.32 (0.27), residues: 378 sheet: -0.65 (0.20), residues: 646 loop : -1.11 (0.16), residues: 1439 *********************** 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 314 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 273 time to evaluate : 2.295 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 outliers start: 41 outliers final: 18 residues processed: 306 average time/residue: 0.3101 time to fit residues: 148.5330 Evaluate side-chains 271 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 2.034 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1893 time to fit residues: 9.1732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 106 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 117 optimal weight: 0.4980 chunk 212 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN N 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 20633 Z= 0.198 Angle : 0.678 13.099 28064 Z= 0.345 Chirality : 0.044 0.225 3374 Planarity : 0.004 0.056 3469 Dihedral : 5.983 30.802 2665 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.52 % Favored : 94.15 % Rotamer Outliers : 1.63 % 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: -0.87 (0.17), residues: 2463 helix: 0.72 (0.27), residues: 369 sheet: -0.30 (0.20), residues: 621 loop : -1.05 (0.16), residues: 1473 *********************** 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 318 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 283 time to evaluate : 2.542 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 outliers start: 35 outliers final: 18 residues processed: 308 average time/residue: 0.3070 time to fit residues: 148.8477 Evaluate side-chains 271 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1849 time to fit residues: 9.2478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN B 540 GLN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 271 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 20633 Z= 0.201 Angle : 0.662 13.084 28064 Z= 0.336 Chirality : 0.044 0.182 3374 Planarity : 0.004 0.057 3469 Dihedral : 5.770 29.659 2665 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.56 % Favored : 94.11 % Rotamer Outliers : 1.73 % 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: -0.78 (0.17), residues: 2463 helix: 0.82 (0.27), residues: 381 sheet: -0.27 (0.20), residues: 623 loop : -1.00 (0.17), residues: 1459 *********************** 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 309 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 272 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 300 average time/residue: 0.3082 time to fit residues: 145.2143 Evaluate side-chains 269 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 2.069 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1848 time to fit residues: 10.9353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 ASN F 241 ASN F 352 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 ** K 417 GLN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 20633 Z= 0.362 Angle : 0.756 13.050 28064 Z= 0.382 Chirality : 0.047 0.213 3374 Planarity : 0.005 0.075 3469 Dihedral : 6.018 29.729 2665 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.75 % Favored : 91.92 % Rotamer Outliers : 1.49 % 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: -0.89 (0.17), residues: 2463 helix: 0.58 (0.27), residues: 390 sheet: -0.40 (0.20), residues: 641 loop : -1.00 (0.17), residues: 1432 *********************** 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 278 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 276 average time/residue: 0.3208 time to fit residues: 137.7155 Evaluate side-chains 248 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 2.091 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2954 time to fit residues: 9.7561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 20633 Z= 0.267 Angle : 0.697 12.707 28064 Z= 0.354 Chirality : 0.045 0.181 3374 Planarity : 0.004 0.057 3469 Dihedral : 5.922 30.322 2665 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.37 % Favored : 93.30 % Rotamer Outliers : 0.98 % 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: -0.72 (0.17), residues: 2463 helix: 0.87 (0.27), residues: 384 sheet: -0.25 (0.21), residues: 588 loop : -0.94 (0.17), residues: 1491 *********************** 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 267 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 266 average time/residue: 0.3155 time to fit residues: 131.3387 Evaluate side-chains 243 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 2.184 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2083 time to fit residues: 5.7388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 186 optimal weight: 0.5980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN ** 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 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 20633 Z= 0.177 Angle : 0.650 12.274 28064 Z= 0.331 Chirality : 0.044 0.179 3374 Planarity : 0.004 0.055 3469 Dihedral : 5.674 29.960 2665 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.09 % Favored : 93.63 % Rotamer Outliers : 0.93 % 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: -0.58 (0.17), residues: 2463 helix: 1.00 (0.28), residues: 390 sheet: -0.00 (0.21), residues: 568 loop : -0.92 (0.17), residues: 1505 *********************** 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 284 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 264 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 280 average time/residue: 0.3179 time to fit residues: 140.0817 Evaluate side-chains 260 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1897 time to fit residues: 6.5005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 0.5980 chunk 227 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 208 optimal weight: 0.4980 chunk 145 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN G 540 GLN ** 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** L 616 ASN N 292 HIS ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 20633 Z= 0.378 Angle : 0.767 12.211 28064 Z= 0.387 Chirality : 0.047 0.237 3374 Planarity : 0.005 0.055 3469 Dihedral : 5.996 29.722 2665 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.04 % Favored : 91.72 % Rotamer Outliers : 0.84 % 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: -0.86 (0.17), residues: 2463 helix: 0.56 (0.27), residues: 405 sheet: -0.35 (0.21), residues: 592 loop : -0.99 (0.17), residues: 1466 *********************** 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 270 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 265 average time/residue: 0.3305 time to fit residues: 136.0047 Evaluate side-chains 250 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 241 time to evaluate : 2.299 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2079 time to fit residues: 6.4671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 1.9990 chunk 142 optimal weight: 0.0370 chunk 110 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 245 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS ** 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 301 ASN N 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3445 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= 0.192 Angle : 0.672 12.287 28064 Z= 0.341 Chirality : 0.044 0.212 3374 Planarity : 0.004 0.055 3469 Dihedral : 5.756 30.368 2665 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.72 % Favored : 94.03 % Rotamer Outliers : 0.09 % 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: -0.62 (0.17), residues: 2463 helix: 1.02 (0.28), residues: 387 sheet: -0.11 (0.21), residues: 562 loop : -0.92 (0.17), residues: 1514 ********************** 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 262 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 260 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 261 average time/residue: 0.3464 time to fit residues: 140.2133 Evaluate side-chains 251 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1959 time to fit residues: 3.7208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 246 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148260 restraints weight = 28426.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143287 restraints weight = 40540.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141183 restraints weight = 36389.382| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 20633 Z= 0.308 Angle : 0.721 12.006 28064 Z= 0.364 Chirality : 0.046 0.206 3374 Planarity : 0.005 0.053 3469 Dihedral : 5.879 30.341 2665 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.55 % Favored : 92.20 % Rotamer Outliers : 0.47 % 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: -0.75 (0.17), residues: 2463 helix: 0.67 (0.27), residues: 405 sheet: -0.20 (0.21), residues: 562 loop : -0.95 (0.17), residues: 1496 =============================================================================== Job complete usr+sys time: 3718.24 seconds wall clock time: 69 minutes 31.41 seconds (4171.41 seconds total)