Starting phenix.real_space_refine on Mon Mar 18 06:46:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb2_40288/03_2024/8sb2_40288_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb2_40288/03_2024/8sb2_40288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb2_40288/03_2024/8sb2_40288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb2_40288/03_2024/8sb2_40288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb2_40288/03_2024/8sb2_40288_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb2_40288/03_2024/8sb2_40288_neut.pdb" } resolution = 3.5 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= 0.010 sd= 0.240 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 12585 2.51 5 N 3321 2.21 5 O 4139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 47": "OE1" <-> "OE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 482": "OE1" <-> "OE2" Residue "G ASP 589": "OD1" <-> "OD2" Residue "G GLU 621": "OE1" <-> "OE2" Residue "G GLU 657": "OE1" <-> "OE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "K TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 657": "OE1" <-> "OE2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 115": "OD1" <-> "OD2" Residue "N GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20186 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} 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: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} 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: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} 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: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" 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: "Z" 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: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.85, per 1000 atoms: 0.54 Number of scatterers: 20186 At special positions: 0 Unit cell: (159.84, 156.6, 139.32, 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 4139 8.00 N 3321 7.00 C 12585 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " 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=2.03 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 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 101 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 101 " 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 Atom "HETATM19206 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN O 8 " - " MAN O 9 " " MAN O 10 " - " MAN O 11 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN T 10 " - " MAN T 11 " " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " MAN P 4 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-6 " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 10 " " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 10 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 5 " 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 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG E 1 " - " ASN A 138 " " NAG J 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 442 " " NAG R 1 " - " ASN F 138 " " NAG S 1 " - " ASN F 301 " " NAG T 1 " - " ASN F 332 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 442 " " NAG W 1 " - " ASN K 138 " " NAG X 1 " - " ASN K 301 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 156 " " NAG a 1 " - " ASN K 442 " Time building additional restraints: 9.58 Conformation dependent library (CDL) restraints added in 3.7 seconds 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4554 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 45 sheets defined 17.4% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.680A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 3.797A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.503A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.734A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.893A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.602A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.631A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.233A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 Processing helix chain 'B' and resid 649 through 663 removed outlier: 3.985A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.941A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.677A pdb=" N ALA F 60 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 74 removed outlier: 3.787A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA F 73 " --> pdb=" O TRP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.537A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.736A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.765A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 596 removed outlier: 3.632A pdb=" N GLN G 575 " --> pdb=" O TRP G 571 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG G 585 " --> pdb=" O LEU G 581 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 593 " --> pdb=" O ASP G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.680A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.030A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 646 Processing helix chain 'G' and resid 650 through 654 Processing helix chain 'G' and resid 655 through 662 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.525A pdb=" N ASP I 84 " --> pdb=" O GLN I 81 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.692A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 74 removed outlier: 3.791A pdb=" N HIS K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA K 73 " --> pdb=" O TRP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 115 Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 475 through 481 removed outlier: 3.767A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 543 removed outlier: 3.926A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.565A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN L 577 " --> pdb=" O ILE L 573 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG L 585 " --> pdb=" O LEU L 581 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP L 589 " --> pdb=" O ARG L 585 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L 593 " --> pdb=" O ASP L 589 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY L 594 " --> pdb=" O GLN L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 removed outlier: 3.650A pdb=" N SER L 615 " --> pdb=" O SER L 612 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.148A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 646 Processing helix chain 'L' and resid 649 through 663 removed outlier: 3.659A pdb=" N GLN L 653 " --> pdb=" O SER L 649 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.550A pdb=" N ASP N 84 " --> pdb=" O GLN N 81 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.063A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 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 177 removed outlier: 6.694A pdb=" N MET A 154 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 134 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.621A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.545A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.841A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.127A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.841A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 308 removed outlier: 5.637A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 361 removed outlier: 3.600A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.151A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.526A pdb=" N THR D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.526A pdb=" N THR D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.495A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.514A pdb=" N LEU F 84 " --> pdb=" O THR F 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 177 removed outlier: 6.759A pdb=" N MET F 154 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA F 134 " --> pdb=" O MET F 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.560A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.568A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.046A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.587A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 359 through 361 removed outlier: 3.597A pdb=" N GLY F 393 " --> pdb=" O TYR F 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.016A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.511A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.511A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 17 through 23 removed outlier: 3.541A pdb=" N THR I 72 " --> pdb=" O SER I 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.242A pdb=" N VAL L 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL K 38 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR L 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR K 40 " --> pdb=" O CYS L 604 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS L 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'K' and resid 75 through 76 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 177 removed outlier: 6.682A pdb=" N MET K 154 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA K 134 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.540A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 259 through 261 removed outlier: 6.569A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.032A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AE4, first strand: chain 'K' and resid 359 through 361 removed outlier: 3.631A pdb=" N GLY K 393 " --> pdb=" O TYR K 361 " (cutoff:3.500A) 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 10 through 12 removed outlier: 5.170A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.524A pdb=" N THR N 108 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL N 35 " --> pdb=" O TYR N 51 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR N 51 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.524A pdb=" N THR N 108 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.537A pdb=" N THR N 72 " --> pdb=" O SER N 69 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1821 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: 8.59 Time building geometry restraints manager: 10.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6211 1.34 - 1.46: 5249 1.46 - 1.59: 8953 1.59 - 1.71: 1 1.71 - 1.84: 192 Bond restraints: 20606 Sorted by residual: bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 3.01e+01 bond pdb=" C THR F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.76e+01 bond pdb=" C1 MAN T 11 " pdb=" C2 MAN T 11 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C5 MAN Y 7 " pdb=" O5 MAN Y 7 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C5 MAN O 7 " pdb=" O5 MAN O 7 " ideal model delta sigma weight residual 1.418 1.481 -0.063 2.00e-02 2.50e+03 9.78e+00 ... (remaining 20601 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.64: 439 105.64 - 113.45: 11755 113.45 - 121.26: 9819 121.26 - 129.06: 5834 129.06 - 136.87: 182 Bond angle restraints: 28029 Sorted by residual: angle pdb=" C ASN K 138 " pdb=" CA ASN K 138 " pdb=" CB ASN K 138 " ideal model delta sigma weight residual 111.82 120.72 -8.90 1.28e+00 6.10e-01 4.84e+01 angle pdb=" N ASP D 33 " pdb=" CA ASP D 33 " pdb=" C ASP D 33 " ideal model delta sigma weight residual 113.17 104.56 8.61 1.26e+00 6.30e-01 4.67e+01 angle pdb=" N ASP N 33 " pdb=" CA ASP N 33 " pdb=" C ASP N 33 " ideal model delta sigma weight residual 113.17 104.71 8.46 1.26e+00 6.30e-01 4.51e+01 angle pdb=" N SER B 649 " pdb=" CA SER B 649 " pdb=" C SER B 649 " ideal model delta sigma weight residual 110.06 119.45 -9.39 1.43e+00 4.89e-01 4.31e+01 angle pdb=" N ASP I 33 " pdb=" CA ASP I 33 " pdb=" C ASP I 33 " ideal model delta sigma weight residual 113.28 105.37 7.91 1.22e+00 6.72e-01 4.21e+01 ... (remaining 28024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 12606 23.11 - 46.21: 493 46.21 - 69.31: 101 69.31 - 92.42: 97 92.42 - 115.52: 48 Dihedral angle restraints: 13345 sinusoidal: 6220 harmonic: 7125 Sorted by residual: dihedral pdb=" CB CYS K 501 " pdb=" SG CYS K 501 " pdb=" SG CYS L 605 " pdb=" CB CYS L 605 " ideal model delta sinusoidal sigma weight residual 93.00 27.72 65.28 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA GLY K 431 " pdb=" C GLY K 431 " pdb=" N ARG K 432 " pdb=" CA ARG K 432 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -146.90 -33.10 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 13342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2710 0.070 - 0.139: 554 0.139 - 0.209: 100 0.209 - 0.278: 22 0.278 - 0.348: 12 Chirality restraints: 3398 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.62e+00 chirality pdb=" CB VAL L 513 " pdb=" CA VAL L 513 " pdb=" CG1 VAL L 513 " pdb=" CG2 VAL L 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 138 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 3395 not shown) Planarity restraints: 3471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.001 2.00e-02 2.50e+03 6.40e-02 5.12e+01 pdb=" CG ASN A 138 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 156 " -0.027 2.00e-02 2.50e+03 2.46e-02 7.58e+00 pdb=" CG ASN K 156 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN K 156 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN K 156 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG Z 1 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 178 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO F 179 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 179 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 179 " 0.038 5.00e-02 4.00e+02 ... (remaining 3468 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4545 2.79 - 3.32: 17566 3.32 - 3.85: 32311 3.85 - 4.37: 37854 4.37 - 4.90: 66433 Nonbonded interactions: 158709 Sorted by model distance: nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.266 2.440 nonbonded pdb=" OD2 ASP K 325 " pdb=" OH TYR M 33 " model vdw 2.271 2.440 nonbonded pdb=" O MET K 369 " pdb=" OG1 THR K 373 " model vdw 2.273 2.440 nonbonded pdb=" O MET F 369 " pdb=" OG1 THR F 373 " model vdw 2.273 2.440 nonbonded pdb=" OH TYR N 48 " pdb=" O3 MAN Y 5 " model vdw 2.288 2.440 ... (remaining 158704 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' selection = chain 'K' } 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 'J' selection = chain 'U' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'R' selection = chain 'V' selection = chain 'W' } 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: 1.750 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: 6.840 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 57.400 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 0.075 20606 Z= 0.398 Angle : 1.100 15.074 28029 Z= 0.578 Chirality : 0.063 0.348 3398 Planarity : 0.007 0.087 3456 Dihedral : 16.754 115.525 8656 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2454 helix: -2.95 (0.20), residues: 375 sheet: -0.06 (0.19), residues: 744 loop : -1.71 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 45 HIS 0.010 0.001 HIS M 116 PHE 0.012 0.002 PHE K 376 TYR 0.024 0.002 TYR M 27 ARG 0.017 0.001 ARG L 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8965 (mtp) cc_final: 0.8618 (mtp) REVERT: A 426 MET cc_start: 0.7231 (ptt) cc_final: 0.6370 (tpt) REVERT: C 25 SER cc_start: 0.7710 (p) cc_final: 0.6851 (p) REVERT: F 34 LEU cc_start: 0.6165 (mt) cc_final: 0.5913 (pt) REVERT: L 584 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7585 (mm-30) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3235 time to fit residues: 120.8019 Evaluate side-chains 178 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 0.1980 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS C 13 ASN C 52 ASN F 105 HIS F 374 HIS G 543 ASN K 105 HIS K 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20606 Z= 0.229 Angle : 0.682 9.716 28029 Z= 0.345 Chirality : 0.048 0.239 3398 Planarity : 0.005 0.052 3456 Dihedral : 12.376 91.569 4276 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 1.46 % Allowed : 6.34 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.63 (0.16), residues: 2454 helix: -2.31 (0.22), residues: 372 sheet: 0.06 (0.19), residues: 711 loop : -1.34 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 50 HIS 0.004 0.001 HIS M 35 PHE 0.013 0.002 PHE N 93 TYR 0.025 0.002 TYR I 51 ARG 0.003 0.000 ARG G 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9028 (mtp) cc_final: 0.8739 (mtp) REVERT: A 426 MET cc_start: 0.7097 (ptt) cc_final: 0.6568 (tpt) REVERT: I 33 ASP cc_start: 0.7714 (t0) cc_final: 0.7472 (t0) REVERT: L 584 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7704 (mm-30) outliers start: 31 outliers final: 24 residues processed: 213 average time/residue: 0.3084 time to fit residues: 102.6755 Evaluate side-chains 193 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 221 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN G 577 GLN ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20606 Z= 0.401 Angle : 0.768 9.858 28029 Z= 0.388 Chirality : 0.051 0.233 3398 Planarity : 0.005 0.056 3456 Dihedral : 11.015 93.572 4276 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.11 % Favored : 93.60 % Rotamer: Outliers : 2.72 % Allowed : 10.42 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.71 (0.16), residues: 2454 helix: -2.28 (0.23), residues: 393 sheet: -0.10 (0.19), residues: 741 loop : -1.37 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 45 HIS 0.006 0.002 HIS H 35 PHE 0.016 0.003 PHE N 93 TYR 0.026 0.002 TYR I 51 ARG 0.006 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 178 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9040 (mtp) cc_final: 0.8546 (mtp) REVERT: F 374 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.7688 (t-170) REVERT: I 33 ASP cc_start: 0.7825 (t0) cc_final: 0.7575 (t0) outliers start: 58 outliers final: 42 residues processed: 216 average time/residue: 0.2856 time to fit residues: 98.7982 Evaluate side-chains 206 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 115 optimal weight: 0.5980 chunk 210 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20606 Z= 0.212 Angle : 0.641 9.638 28029 Z= 0.323 Chirality : 0.047 0.187 3398 Planarity : 0.004 0.044 3456 Dihedral : 9.691 85.570 4276 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.09 % Favored : 94.62 % Rotamer: Outliers : 2.63 % Allowed : 12.91 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.50 (0.17), residues: 2454 helix: -1.75 (0.25), residues: 372 sheet: -0.15 (0.18), residues: 756 loop : -1.24 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS F 72 PHE 0.011 0.002 PHE F 391 TYR 0.019 0.001 TYR I 48 ARG 0.005 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 172 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9029 (mtp) cc_final: 0.8709 (mtp) outliers start: 56 outliers final: 40 residues processed: 205 average time/residue: 0.2874 time to fit residues: 95.6458 Evaluate side-chains 204 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 chunk 200 optimal weight: 0.2980 chunk 162 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20606 Z= 0.175 Angle : 0.611 9.762 28029 Z= 0.308 Chirality : 0.045 0.176 3398 Planarity : 0.004 0.040 3456 Dihedral : 8.906 81.526 4276 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.26 % Favored : 94.46 % Rotamer: Outliers : 3.00 % Allowed : 13.52 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.29 (0.17), residues: 2454 helix: -1.36 (0.26), residues: 363 sheet: -0.14 (0.18), residues: 753 loop : -1.11 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.003 0.001 HIS F 72 PHE 0.009 0.001 PHE F 317 TYR 0.018 0.001 TYR I 48 ARG 0.005 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 173 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9034 (mtp) cc_final: 0.8679 (mtp) REVERT: D 92 SER cc_start: 0.8701 (t) cc_final: 0.8480 (t) REVERT: F 348 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: G 530 MET cc_start: 0.8144 (mmm) cc_final: 0.7257 (mtt) outliers start: 64 outliers final: 46 residues processed: 215 average time/residue: 0.2865 time to fit residues: 99.5836 Evaluate side-chains 215 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 369 MET Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.7980 chunk 211 optimal weight: 0.0870 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 0.4980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20606 Z= 0.158 Angle : 0.602 11.380 28029 Z= 0.300 Chirality : 0.045 0.196 3398 Planarity : 0.004 0.037 3456 Dihedral : 8.304 76.577 4276 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.77 % Favored : 94.95 % Rotamer: Outliers : 3.10 % Allowed : 14.13 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.15 (0.17), residues: 2454 helix: -1.12 (0.26), residues: 372 sheet: 0.01 (0.19), residues: 738 loop : -1.07 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.000 HIS F 72 PHE 0.009 0.001 PHE F 317 TYR 0.017 0.001 TYR I 48 ARG 0.007 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 180 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9060 (mtp) cc_final: 0.8689 (mtp) REVERT: D 92 SER cc_start: 0.8684 (t) cc_final: 0.8473 (t) REVERT: G 530 MET cc_start: 0.8040 (mmm) cc_final: 0.7273 (mtt) outliers start: 66 outliers final: 49 residues processed: 225 average time/residue: 0.2836 time to fit residues: 103.2385 Evaluate side-chains 221 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 172 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 197 optimal weight: 0.3980 chunk 131 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20606 Z= 0.203 Angle : 0.622 11.044 28029 Z= 0.313 Chirality : 0.046 0.201 3398 Planarity : 0.004 0.037 3456 Dihedral : 8.242 76.195 4276 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.26 % Favored : 94.46 % Rotamer: Outliers : 2.96 % Allowed : 14.51 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.09 (0.17), residues: 2454 helix: -0.95 (0.26), residues: 363 sheet: -0.07 (0.18), residues: 753 loop : -1.00 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE F 317 TYR 0.018 0.001 TYR I 48 ARG 0.007 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 175 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9070 (mtp) cc_final: 0.8699 (mtp) REVERT: D 92 SER cc_start: 0.8682 (t) cc_final: 0.8456 (t) REVERT: F 348 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: G 530 MET cc_start: 0.8089 (mmm) cc_final: 0.7218 (mtt) REVERT: G 654 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7717 (tp30) REVERT: K 112 TRP cc_start: 0.7750 (t-100) cc_final: 0.7515 (t-100) REVERT: K 348 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7086 (mp0) outliers start: 63 outliers final: 55 residues processed: 215 average time/residue: 0.2858 time to fit residues: 98.5862 Evaluate side-chains 230 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 173 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20606 Z= 0.290 Angle : 0.677 11.788 28029 Z= 0.339 Chirality : 0.048 0.529 3398 Planarity : 0.004 0.041 3456 Dihedral : 8.546 79.437 4276 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.91 % Favored : 93.81 % Rotamer: Outliers : 3.10 % Allowed : 14.88 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.21 (0.17), residues: 2454 helix: -1.13 (0.26), residues: 369 sheet: -0.05 (0.18), residues: 783 loop : -1.15 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 45 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.002 PHE F 317 TYR 0.019 0.002 TYR I 48 ARG 0.007 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 173 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 SER cc_start: 0.8702 (t) cc_final: 0.8456 (t) REVERT: G 530 MET cc_start: 0.8171 (mmm) cc_final: 0.7346 (mtt) REVERT: G 654 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7792 (tp30) REVERT: K 112 TRP cc_start: 0.7760 (t-100) cc_final: 0.7556 (t-100) REVERT: M 3 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7725 (pt0) outliers start: 66 outliers final: 60 residues processed: 213 average time/residue: 0.2810 time to fit residues: 95.9036 Evaluate side-chains 232 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 171 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20606 Z= 0.308 Angle : 0.697 12.313 28029 Z= 0.347 Chirality : 0.050 0.501 3398 Planarity : 0.004 0.041 3456 Dihedral : 8.650 82.108 4276 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.15 % Favored : 93.56 % Rotamer: Outliers : 3.38 % Allowed : 14.88 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.34 (0.17), residues: 2454 helix: -1.34 (0.25), residues: 390 sheet: -0.10 (0.18), residues: 783 loop : -1.20 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 96 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.002 PHE F 317 TYR 0.019 0.002 TYR I 48 ARG 0.007 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 177 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9025 (mtp) cc_final: 0.8528 (mtp) REVERT: A 475 MET cc_start: 0.8291 (tpp) cc_final: 0.8065 (tpp) REVERT: D 92 SER cc_start: 0.8734 (t) cc_final: 0.8512 (t) REVERT: G 530 MET cc_start: 0.8231 (mmm) cc_final: 0.7423 (mtt) REVERT: G 654 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7760 (tp30) REVERT: M 3 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7738 (pt0) outliers start: 72 outliers final: 64 residues processed: 221 average time/residue: 0.2797 time to fit residues: 99.5027 Evaluate side-chains 236 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 171 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20606 Z= 0.219 Angle : 0.657 12.689 28029 Z= 0.330 Chirality : 0.055 1.233 3398 Planarity : 0.004 0.041 3456 Dihedral : 8.622 79.479 4276 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.50 % Favored : 94.21 % Rotamer: Outliers : 2.77 % Allowed : 15.45 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.18 (0.17), residues: 2454 helix: -1.06 (0.26), residues: 369 sheet: -0.08 (0.18), residues: 789 loop : -1.10 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 50 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.002 PHE A 391 TYR 0.018 0.001 TYR I 48 ARG 0.011 0.000 ARG B 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 174 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9009 (mtp) cc_final: 0.8685 (mtp) REVERT: D 92 SER cc_start: 0.8736 (t) cc_final: 0.8500 (t) REVERT: G 530 MET cc_start: 0.8180 (mmm) cc_final: 0.7371 (mtt) REVERT: M 3 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7725 (pt0) outliers start: 59 outliers final: 58 residues processed: 211 average time/residue: 0.2931 time to fit residues: 98.5118 Evaluate side-chains 231 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 172 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 625 ASN Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.163586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.158007 restraints weight = 29162.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.147312 restraints weight = 57840.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143856 restraints weight = 51760.083| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20606 Z= 0.410 Angle : 0.767 13.092 28029 Z= 0.385 Chirality : 0.057 1.080 3398 Planarity : 0.005 0.044 3456 Dihedral : 9.365 89.079 4276 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.21 % Favored : 92.50 % Rotamer: Outliers : 3.15 % Allowed : 15.26 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.63 (0.17), residues: 2454 helix: -1.69 (0.24), residues: 405 sheet: -0.20 (0.18), residues: 783 loop : -1.41 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 96 HIS 0.005 0.001 HIS K 105 PHE 0.018 0.003 PHE K 383 TYR 0.020 0.002 TYR I 48 ARG 0.005 0.001 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.30 seconds wall clock time: 60 minutes 42.41 seconds (3642.41 seconds total)