Starting phenix.real_space_refine on Tue Apr 9 09:08:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8e_23231/04_2024/7l8e_23231_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8e_23231/04_2024/7l8e_23231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8e_23231/04_2024/7l8e_23231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8e_23231/04_2024/7l8e_23231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8e_23231/04_2024/7l8e_23231_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8e_23231/04_2024/7l8e_23231_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 102 5.16 5 C 9840 2.51 5 N 2662 2.21 5 O 3223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15827 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3506 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 3 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3486 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1003 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "G" 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: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.58, per 1000 atoms: 0.54 Number of scatterers: 15827 At special positions: 0 Unit cell: (133.9, 127.72, 142.14, 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 102 16.00 O 3223 8.00 N 2662 7.00 C 9840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.08 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.09 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA X 3 " - " MAN X 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 295 " " NAG A 704 " - " ASN A 386 " " NAG A 705 " - " ASN A 363 " " NAG A 706 " - " ASN A 234 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 241 " " NAG A 709 " - " ASN A 289 " " NAG A 710 " - " ASN A 339 " " NAG A 711 " - " ASN A 355 " " NAG A 712 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 276 " " NAG C 703 " - " ASN C 386 " " NAG C 704 " - " ASN C 363 " " NAG C 705 " - " ASN C 133 " " NAG C 706 " - " ASN C 88 " " NAG C 707 " - " ASN C 241 " " NAG C 708 " - " ASN C 289 " " NAG C 709 " - " ASN C 339 " " NAG C 710 " - " ASN C 355 " " NAG C 711 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 701 " - " ASN E 160 " " NAG E 702 " - " ASN E 276 " " NAG E 703 " - " ASN E 386 " " NAG E 704 " - " ASN E 363 " " NAG E 705 " - " ASN E 234 " " NAG E 706 " - " ASN E 133 " " NAG E 707 " - " ASN E 301 " " NAG E 708 " - " ASN E 88 " " NAG E 709 " - " ASN E 289 " " NAG E 710 " - " ASN E 339 " " NAG E 711 " - " ASN E 355 " " NAG E 712 " - " ASN E 392 " " NAG E 713 " - " ASN E 137 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 448 " " NAG J 1 " - " ASN C 295 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 448 " " NAG S 1 " - " ASN E 295 " " NAG T 1 " - " ASN E 197 " " NAG U 1 " - " ASN E 156 " " NAG V 1 " - " ASN E 241 " " NAG W 1 " - " ASN E 332 " " NAG X 1 " - " ASN A 262 " " NAG Y 1 " - " ASN A 448 " " NAG Z 1 " - " ASN A 197 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 88 " " NAG c 1 " - " ASN A 332 " Time building additional restraints: 6.93 Conformation dependent library (CDL) restraints added in 2.5 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 30 sheets defined 26.4% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.379A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'D' and resid 524 through 527 removed outlier: 4.319A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 532 through 542 removed outlier: 5.105A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 540 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 541 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 542 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 639 through 660 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 353 removed outlier: 4.025A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 475 through 485 removed outlier: 3.600A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 483 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.197A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 532 through 544 removed outlier: 4.974A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 639 through 663 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.090A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.574A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 543 removed outlier: 5.236A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 542 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 622 No H-bonds generated for 'chain 'B' and resid 619 through 622' Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 660 Processing helix chain 'L' and resid 26 through 30 Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.864A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.762A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.697A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.738A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 443 through 449 removed outlier: 7.791A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 305 through 308 Processing sheet with id= I, first strand: chain 'C' and resid 465 through 467 removed outlier: 6.221A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= K, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= N, first strand: chain 'E' and resid 169 through 177 Processing sheet with id= O, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= P, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 305 through 312 removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= T, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= U, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= V, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= W, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= X, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.825A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.247A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.837A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 301 through 308 removed outlier: 4.373A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 33 through 36 Processing sheet with id= AC, first strand: chain 'L' and resid 19 through 24 Processing sheet with id= AD, first strand: chain 'L' and resid 34 through 38 527 hydrogen bonds defined for protein. 1365 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: 4.96 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3760 1.32 - 1.46: 4949 1.46 - 1.60: 7232 1.60 - 1.74: 25 1.74 - 1.88: 132 Bond restraints: 16098 Sorted by residual: bond pdb=" CB TYR C 319 " pdb=" CG TYR C 319 " ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.59e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.21e+01 bond pdb=" CB TYR E 484 " pdb=" CG TYR E 484 " ideal model delta sigma weight residual 1.512 1.371 0.141 2.20e-02 2.07e+03 4.11e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.03e+01 bond pdb=" NE1 TRP D 628 " pdb=" CE2 TRP D 628 " ideal model delta sigma weight residual 1.370 1.311 0.059 1.10e-02 8.26e+03 2.89e+01 ... (remaining 16093 not shown) Histogram of bond angle deviations from ideal: 95.10 - 103.15: 150 103.15 - 111.21: 6961 111.21 - 119.26: 7149 119.26 - 127.31: 7414 127.31 - 135.36: 220 Bond angle restraints: 21894 Sorted by residual: angle pdb=" C VAL C 75 " pdb=" N PRO C 76 " pdb=" CA PRO C 76 " ideal model delta sigma weight residual 119.56 128.63 -9.07 1.02e+00 9.61e-01 7.91e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.61 -9.05 1.02e+00 9.61e-01 7.86e+01 angle pdb=" N PRO A 437 " pdb=" CA PRO A 437 " pdb=" C PRO A 437 " ideal model delta sigma weight residual 110.47 101.99 8.48 9.60e-01 1.09e+00 7.80e+01 angle pdb=" C GLY A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta sigma weight residual 119.78 128.60 -8.82 1.03e+00 9.43e-01 7.34e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 128.19 -8.63 1.02e+00 9.61e-01 7.16e+01 ... (remaining 21889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 10551 21.23 - 42.47: 230 42.47 - 63.70: 76 63.70 - 84.93: 27 84.93 - 106.17: 19 Dihedral angle restraints: 10903 sinusoidal: 5362 harmonic: 5541 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -131.82 45.82 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" C ASN D 637 " pdb=" N ASN D 637 " pdb=" CA ASN D 637 " pdb=" CB ASN D 637 " ideal model delta harmonic sigma weight residual -122.60 -110.19 -12.41 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.96 40.96 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 10900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1779 0.101 - 0.202: 613 0.202 - 0.303: 226 0.303 - 0.404: 106 0.404 - 0.505: 69 Chirality restraints: 2793 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.43e+02 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.41e+02 ... (remaining 2790 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.344 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG Z 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " 0.341 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG X 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.333 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG B 702 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.083 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3202 2.78 - 3.31: 15185 3.31 - 3.84: 25758 3.84 - 4.37: 31399 4.37 - 4.90: 48747 Nonbonded interactions: 124291 Sorted by model distance: nonbonded pdb=" O3 NAG X 1 " pdb=" O7 NAG X 1 " model vdw 2.253 2.440 nonbonded pdb=" O ASP A 325 " pdb=" OD1 ASP A 325 " model vdw 2.362 3.040 nonbonded pdb=" O3 NAG C 702 " pdb=" O7 NAG C 702 " model vdw 2.376 2.440 nonbonded pdb=" N TYR D 638 " pdb=" N THR D 639 " model vdw 2.386 2.560 nonbonded pdb=" NZ LYS E 46 " pdb=" OD2 ASP F 632 " model vdw 2.396 2.520 ... (remaining 124286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 56 or resid 66 through 397 or resid 411 through \ 505 or resid 702 through 712)) selection = (chain 'C' and (resid 33 through 56 or resid 66 through 505 or resid 701 through \ 711)) selection = (chain 'E' and (resid 33 through 56 or resid 66 through 505 or resid 702 through \ 712)) } ncs_group { reference = (chain 'B' and (resid 520 through 661 or resid 702 through 703)) selection = (chain 'D' and (resid 520 through 546 or resid 568 through 661 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 520 through 546 or resid 568 through 661 or resid 702 thro \ ugh 703)) } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = (chain 'H' and resid 14 through 112) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 1.570 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: 7.940 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.570 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.022 0.164 16098 Z= 1.377 Angle : 1.739 15.659 21894 Z= 1.118 Chirality : 0.145 0.505 2793 Planarity : 0.018 0.295 2680 Dihedral : 11.274 106.167 7200 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 1666 helix: 0.42 (0.23), residues: 418 sheet: 1.17 (0.24), residues: 402 loop : 0.87 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.010 TRP E 35 HIS 0.011 0.002 HIS C 374 PHE 0.035 0.006 PHE C 233 TYR 0.052 0.009 TYR C 40 ARG 0.008 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 LEU cc_start: 0.9469 (mt) cc_final: 0.9233 (mt) REVERT: C 338 TRP cc_start: 0.9142 (t-100) cc_final: 0.8681 (t-100) REVERT: C 390 LEU cc_start: 0.9577 (mt) cc_final: 0.8960 (mt) REVERT: C 486 TYR cc_start: 0.8927 (m-80) cc_final: 0.8429 (m-80) REVERT: D 574 LYS cc_start: 0.9264 (mttt) cc_final: 0.8961 (mttp) REVERT: D 606 THR cc_start: 0.8589 (p) cc_final: 0.8293 (t) REVERT: D 634 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8690 (mt-10) REVERT: D 639 THR cc_start: 0.9074 (m) cc_final: 0.8124 (p) REVERT: D 645 LEU cc_start: 0.9087 (mt) cc_final: 0.8153 (mt) REVERT: D 663 LEU cc_start: 0.7999 (tp) cc_final: 0.7721 (tt) REVERT: E 103 GLN cc_start: 0.8707 (tt0) cc_final: 0.8299 (tp40) REVERT: E 107 ASP cc_start: 0.9068 (m-30) cc_final: 0.8841 (m-30) REVERT: E 180 ASP cc_start: 0.9157 (m-30) cc_final: 0.8721 (m-30) REVERT: E 390 LEU cc_start: 0.9637 (mt) cc_final: 0.9208 (mt) REVERT: E 426 MET cc_start: 0.8489 (mtp) cc_final: 0.8229 (mtp) REVERT: E 434 MET cc_start: 0.9490 (ttp) cc_final: 0.9258 (ttp) REVERT: F 543 ASN cc_start: 0.8449 (m-40) cc_final: 0.8127 (m110) REVERT: F 571 TRP cc_start: 0.8890 (t60) cc_final: 0.8686 (t60) REVERT: F 577 GLN cc_start: 0.9069 (mt0) cc_final: 0.8775 (mt0) REVERT: F 639 THR cc_start: 0.8258 (m) cc_final: 0.6095 (p) REVERT: A 180 ASP cc_start: 0.8591 (m-30) cc_final: 0.8353 (m-30) REVERT: A 284 ILE cc_start: 0.9606 (mt) cc_final: 0.9329 (pt) REVERT: A 430 ILE cc_start: 0.8933 (mm) cc_final: 0.8715 (tp) REVERT: B 545 LEU cc_start: 0.8794 (mt) cc_final: 0.8198 (mm) REVERT: B 586 TYR cc_start: 0.9318 (t80) cc_final: 0.8733 (t80) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.3124 time to fit residues: 210.6808 Evaluate side-chains 237 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN F 585 HIS A 103 GLN A 137 ASN A 195 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 425 ASN A 462 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16098 Z= 0.254 Angle : 0.755 10.999 21894 Z= 0.386 Chirality : 0.050 0.277 2793 Planarity : 0.004 0.043 2680 Dihedral : 9.419 84.056 3986 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.26 % Allowed : 2.10 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1666 helix: 1.51 (0.27), residues: 393 sheet: 0.86 (0.24), residues: 420 loop : 0.23 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 631 HIS 0.009 0.001 HIS F 585 PHE 0.027 0.002 PHE C 383 TYR 0.048 0.002 TYR F 643 ARG 0.004 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 316 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 201 ILE cc_start: 0.8732 (tt) cc_final: 0.8525 (tt) REVERT: C 384 TYR cc_start: 0.8743 (m-80) cc_final: 0.8519 (m-80) REVERT: C 486 TYR cc_start: 0.8650 (m-80) cc_final: 0.8398 (m-80) REVERT: D 574 LYS cc_start: 0.9354 (mttt) cc_final: 0.8927 (mttp) REVERT: D 577 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 641 ILE cc_start: 0.8276 (mp) cc_final: 0.7884 (tt) REVERT: D 643 TYR cc_start: 0.8311 (m-10) cc_final: 0.8107 (m-80) REVERT: D 645 LEU cc_start: 0.8768 (mt) cc_final: 0.8348 (mt) REVERT: D 656 ASN cc_start: 0.9279 (m-40) cc_final: 0.9059 (m-40) REVERT: E 69 TRP cc_start: 0.8486 (m100) cc_final: 0.8252 (m100) REVERT: E 103 GLN cc_start: 0.8688 (tt0) cc_final: 0.7830 (tp40) REVERT: E 107 ASP cc_start: 0.9006 (m-30) cc_final: 0.8459 (m-30) REVERT: E 217 TYR cc_start: 0.8241 (m-80) cc_final: 0.7409 (m-80) REVERT: E 309 ILE cc_start: 0.9407 (mt) cc_final: 0.8938 (mt) REVERT: E 338 TRP cc_start: 0.8964 (t-100) cc_final: 0.8269 (t-100) REVERT: E 390 LEU cc_start: 0.9525 (mt) cc_final: 0.8916 (mt) REVERT: E 426 MET cc_start: 0.8477 (mtp) cc_final: 0.8091 (mtp) REVERT: E 475 MET cc_start: 0.8448 (mmp) cc_final: 0.8091 (mmp) REVERT: E 504 ARG cc_start: 0.8861 (tpt-90) cc_final: 0.8656 (tpp80) REVERT: F 577 GLN cc_start: 0.8992 (mt0) cc_final: 0.8750 (mt0) REVERT: F 630 GLN cc_start: 0.9096 (mt0) cc_final: 0.8602 (mt0) REVERT: A 155 LYS cc_start: 0.9058 (mttm) cc_final: 0.8774 (mmmm) REVERT: A 180 ASP cc_start: 0.8590 (m-30) cc_final: 0.7973 (m-30) REVERT: A 382 PHE cc_start: 0.9033 (m-80) cc_final: 0.8570 (m-80) REVERT: A 475 MET cc_start: 0.8282 (pmm) cc_final: 0.7850 (pmm) REVERT: B 586 TYR cc_start: 0.9124 (t80) cc_final: 0.8910 (t80) REVERT: B 643 TYR cc_start: 0.9030 (m-10) cc_final: 0.8738 (m-10) REVERT: B 657 GLU cc_start: 0.9204 (tp30) cc_final: 0.8857 (tp30) REVERT: B 661 LEU cc_start: 0.5910 (mt) cc_final: 0.5026 (mt) outliers start: 4 outliers final: 0 residues processed: 317 average time/residue: 0.2922 time to fit residues: 135.6346 Evaluate side-chains 203 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 171 optimal weight: 30.0000 chunk 184 optimal weight: 30.0000 chunk 152 optimal weight: 9.9990 chunk 169 optimal weight: 40.0000 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 330 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 540 GLN F 543 ASN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 616 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16098 Z= 0.411 Angle : 0.784 10.515 21894 Z= 0.397 Chirality : 0.050 0.454 2793 Planarity : 0.005 0.080 2680 Dihedral : 9.085 73.031 3986 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1666 helix: 1.31 (0.26), residues: 394 sheet: 0.46 (0.23), residues: 453 loop : -0.13 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 631 HIS 0.010 0.002 HIS C 352 PHE 0.028 0.003 PHE E 468 TYR 0.027 0.003 TYR F 643 ARG 0.014 0.001 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 217 TYR cc_start: 0.8542 (m-80) cc_final: 0.7871 (m-80) REVERT: C 317 PHE cc_start: 0.9320 (t80) cc_final: 0.8944 (t80) REVERT: C 390 LEU cc_start: 0.9525 (mt) cc_final: 0.9290 (mt) REVERT: D 577 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8658 (tm-30) REVERT: D 656 ASN cc_start: 0.9224 (m-40) cc_final: 0.8947 (m110) REVERT: E 42 VAL cc_start: 0.8258 (t) cc_final: 0.7926 (p) REVERT: E 95 MET cc_start: 0.8552 (ttp) cc_final: 0.7955 (tmm) REVERT: E 217 TYR cc_start: 0.8349 (m-80) cc_final: 0.7722 (m-80) REVERT: E 338 TRP cc_start: 0.9206 (t-100) cc_final: 0.8294 (t-100) REVERT: E 390 LEU cc_start: 0.9659 (mt) cc_final: 0.9061 (mt) REVERT: E 395 TRP cc_start: 0.8301 (m100) cc_final: 0.7878 (m100) REVERT: E 426 MET cc_start: 0.8576 (mtp) cc_final: 0.8219 (mtp) REVERT: F 522 PHE cc_start: 0.9091 (t80) cc_final: 0.8882 (t80) REVERT: F 543 ASN cc_start: 0.8223 (m110) cc_final: 0.7938 (m110) REVERT: F 591 GLN cc_start: 0.9133 (tt0) cc_final: 0.8883 (tt0) REVERT: F 648 GLU cc_start: 0.9210 (tp30) cc_final: 0.8910 (pp20) REVERT: A 35 TRP cc_start: 0.8447 (m100) cc_final: 0.7862 (m100) REVERT: A 180 ASP cc_start: 0.8745 (m-30) cc_final: 0.8121 (m-30) outliers start: 2 outliers final: 1 residues processed: 241 average time/residue: 0.2950 time to fit residues: 105.4752 Evaluate side-chains 170 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 50.0000 chunk 128 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 171 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN E 428 GLN F 585 HIS A 183 GLN A 185 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16098 Z= 0.270 Angle : 0.644 9.306 21894 Z= 0.328 Chirality : 0.046 0.306 2793 Planarity : 0.004 0.050 2680 Dihedral : 8.442 67.458 3986 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1666 helix: 1.47 (0.26), residues: 384 sheet: 0.38 (0.24), residues: 414 loop : -0.24 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP F 631 HIS 0.007 0.001 HIS F 585 PHE 0.019 0.002 PHE E 53 TYR 0.030 0.002 TYR B 643 ARG 0.005 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 217 TYR cc_start: 0.8492 (m-80) cc_final: 0.7731 (m-80) REVERT: C 390 LEU cc_start: 0.9510 (mt) cc_final: 0.9270 (mt) REVERT: C 484 TYR cc_start: 0.8944 (p90) cc_final: 0.8726 (p90) REVERT: D 577 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8651 (tm-30) REVERT: D 643 TYR cc_start: 0.8493 (m-80) cc_final: 0.8128 (m-80) REVERT: D 645 LEU cc_start: 0.8750 (mt) cc_final: 0.8403 (mt) REVERT: D 656 ASN cc_start: 0.9149 (m-40) cc_final: 0.8840 (m110) REVERT: E 95 MET cc_start: 0.8658 (ttp) cc_final: 0.8080 (tmm) REVERT: E 104 MET cc_start: 0.9029 (tpp) cc_final: 0.8328 (tpp) REVERT: E 217 TYR cc_start: 0.8122 (m-80) cc_final: 0.7022 (m-80) REVERT: E 218 CYS cc_start: 0.6897 (m) cc_final: 0.6427 (m) REVERT: E 338 TRP cc_start: 0.9149 (t-100) cc_final: 0.8261 (t-100) REVERT: E 390 LEU cc_start: 0.9645 (mt) cc_final: 0.9059 (mt) REVERT: E 395 TRP cc_start: 0.8250 (m100) cc_final: 0.7894 (m100) REVERT: E 426 MET cc_start: 0.8519 (mtp) cc_final: 0.8317 (mtp) REVERT: F 543 ASN cc_start: 0.8262 (m110) cc_final: 0.8038 (m110) REVERT: F 626 MET cc_start: 0.7161 (tpp) cc_final: 0.6623 (tpp) REVERT: F 648 GLU cc_start: 0.9143 (tp30) cc_final: 0.8941 (pp20) REVERT: F 654 GLU cc_start: 0.8446 (tt0) cc_final: 0.8207 (tp30) REVERT: A 131 CYS cc_start: 0.6336 (m) cc_final: 0.6076 (m) REVERT: A 180 ASP cc_start: 0.8708 (m-30) cc_final: 0.8157 (m-30) REVERT: B 643 TYR cc_start: 0.8676 (m-10) cc_final: 0.8086 (m-80) outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.2901 time to fit residues: 103.3448 Evaluate side-chains 175 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 330 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN D 658 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 540 GLN F 585 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16098 Z= 0.221 Angle : 0.612 9.419 21894 Z= 0.307 Chirality : 0.046 0.276 2793 Planarity : 0.004 0.048 2680 Dihedral : 7.973 62.806 3986 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.07 % Allowed : 1.84 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1666 helix: 1.45 (0.26), residues: 400 sheet: 0.35 (0.24), residues: 424 loop : -0.38 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 479 HIS 0.007 0.001 HIS F 585 PHE 0.018 0.002 PHE A 53 TYR 0.022 0.002 TYR D 643 ARG 0.004 0.000 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 217 TYR cc_start: 0.8549 (m-80) cc_final: 0.7629 (m-80) REVERT: D 577 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8636 (tm-30) REVERT: D 639 THR cc_start: 0.8778 (m) cc_final: 0.7058 (m) REVERT: D 643 TYR cc_start: 0.8478 (m-10) cc_final: 0.8064 (m-80) REVERT: D 645 LEU cc_start: 0.8779 (mt) cc_final: 0.8378 (mt) REVERT: D 652 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8330 (tp-100) REVERT: D 656 ASN cc_start: 0.9112 (m-40) cc_final: 0.8488 (m-40) REVERT: E 95 MET cc_start: 0.8592 (ttp) cc_final: 0.7982 (tmm) REVERT: E 104 MET cc_start: 0.8991 (tpp) cc_final: 0.8423 (tpp) REVERT: E 109 ILE cc_start: 0.9133 (mm) cc_final: 0.8928 (mm) REVERT: E 217 TYR cc_start: 0.8113 (m-80) cc_final: 0.7218 (m-80) REVERT: E 390 LEU cc_start: 0.9639 (mt) cc_final: 0.9268 (mt) REVERT: E 395 TRP cc_start: 0.8249 (m100) cc_final: 0.7805 (m100) REVERT: E 426 MET cc_start: 0.8418 (mtp) cc_final: 0.8142 (mtp) REVERT: E 434 MET cc_start: 0.9228 (ttp) cc_final: 0.8945 (ttp) REVERT: F 571 TRP cc_start: 0.8375 (t60) cc_final: 0.7885 (t60) REVERT: F 626 MET cc_start: 0.7114 (tpp) cc_final: 0.6767 (tpp) REVERT: F 654 GLU cc_start: 0.8470 (tt0) cc_final: 0.8152 (tp30) REVERT: A 180 ASP cc_start: 0.8756 (m-30) cc_final: 0.8189 (m-30) REVERT: B 523 LEU cc_start: 0.8451 (mt) cc_final: 0.8244 (mt) REVERT: B 643 TYR cc_start: 0.8637 (m-10) cc_final: 0.8145 (m-80) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.2750 time to fit residues: 94.0816 Evaluate side-chains 166 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN D 658 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16098 Z= 0.369 Angle : 0.732 9.451 21894 Z= 0.364 Chirality : 0.048 0.251 2793 Planarity : 0.004 0.051 2680 Dihedral : 8.276 56.209 3986 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1666 helix: 1.14 (0.26), residues: 402 sheet: -0.24 (0.23), residues: 450 loop : -0.54 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 45 HIS 0.010 0.002 HIS A 374 PHE 0.021 0.003 PHE E 53 TYR 0.030 0.003 TYR E 217 ARG 0.006 0.001 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 217 TYR cc_start: 0.8566 (m-80) cc_final: 0.7938 (m-80) REVERT: C 390 LEU cc_start: 0.9466 (mt) cc_final: 0.9228 (mt) REVERT: C 486 TYR cc_start: 0.8745 (m-80) cc_final: 0.8537 (m-80) REVERT: D 577 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8730 (tm-30) REVERT: D 645 LEU cc_start: 0.8887 (mt) cc_final: 0.8506 (mt) REVERT: D 652 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8502 (tp-100) REVERT: E 42 VAL cc_start: 0.8423 (t) cc_final: 0.8160 (p) REVERT: E 69 TRP cc_start: 0.9071 (m100) cc_final: 0.8081 (m-10) REVERT: E 95 MET cc_start: 0.8780 (ttp) cc_final: 0.8085 (tmm) REVERT: E 104 MET cc_start: 0.8959 (tpp) cc_final: 0.8607 (tpp) REVERT: E 217 TYR cc_start: 0.8123 (m-80) cc_final: 0.7361 (m-80) REVERT: E 368 ASP cc_start: 0.8933 (p0) cc_final: 0.8660 (p0) REVERT: E 390 LEU cc_start: 0.9679 (mt) cc_final: 0.9263 (mt) REVERT: E 426 MET cc_start: 0.8461 (mtp) cc_final: 0.8087 (mtp) REVERT: E 434 MET cc_start: 0.9255 (ttp) cc_final: 0.8962 (ttp) REVERT: F 571 TRP cc_start: 0.8452 (t60) cc_final: 0.7966 (t60) REVERT: F 654 GLU cc_start: 0.8610 (tt0) cc_final: 0.8180 (tp30) REVERT: A 131 CYS cc_start: 0.6442 (m) cc_final: 0.5952 (m) REVERT: A 180 ASP cc_start: 0.8739 (m-30) cc_final: 0.8185 (m-30) REVERT: B 643 TYR cc_start: 0.8814 (m-10) cc_final: 0.8309 (m-80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2648 time to fit residues: 80.7303 Evaluate side-chains 151 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 113 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN D 658 GLN E 103 GLN F 543 ASN F 585 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16098 Z= 0.240 Angle : 0.624 9.404 21894 Z= 0.314 Chirality : 0.046 0.275 2793 Planarity : 0.004 0.045 2680 Dihedral : 7.833 56.485 3986 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1666 helix: 1.47 (0.27), residues: 396 sheet: -0.13 (0.24), residues: 425 loop : -0.62 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 45 HIS 0.009 0.001 HIS F 585 PHE 0.018 0.002 PHE C 53 TYR 0.021 0.002 TYR D 643 ARG 0.003 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 390 LEU cc_start: 0.9437 (mt) cc_final: 0.9191 (mt) REVERT: C 486 TYR cc_start: 0.8733 (m-80) cc_final: 0.8443 (m-80) REVERT: D 577 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8703 (tm-30) REVERT: D 639 THR cc_start: 0.8657 (m) cc_final: 0.7781 (m) REVERT: D 643 TYR cc_start: 0.8626 (m-80) cc_final: 0.8286 (m-80) REVERT: D 652 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8529 (tp-100) REVERT: E 42 VAL cc_start: 0.8387 (t) cc_final: 0.7980 (m) REVERT: E 69 TRP cc_start: 0.9019 (m100) cc_final: 0.8045 (m-10) REVERT: E 95 MET cc_start: 0.8740 (ttp) cc_final: 0.8070 (tmm) REVERT: E 368 ASP cc_start: 0.8856 (p0) cc_final: 0.8648 (p0) REVERT: E 390 LEU cc_start: 0.9627 (mt) cc_final: 0.9214 (mt) REVERT: E 426 MET cc_start: 0.8483 (mtp) cc_final: 0.8131 (mtp) REVERT: E 434 MET cc_start: 0.9222 (ttp) cc_final: 0.8918 (ttp) REVERT: F 543 ASN cc_start: 0.8051 (m110) cc_final: 0.7847 (m110) REVERT: F 571 TRP cc_start: 0.8355 (t60) cc_final: 0.7892 (t60) REVERT: F 654 GLU cc_start: 0.8573 (tt0) cc_final: 0.8187 (tp30) REVERT: A 69 TRP cc_start: 0.8955 (m100) cc_final: 0.8465 (m-90) REVERT: A 131 CYS cc_start: 0.6372 (m) cc_final: 0.5832 (m) REVERT: A 161 MET cc_start: 0.8524 (ttt) cc_final: 0.8280 (ttt) REVERT: A 180 ASP cc_start: 0.8740 (m-30) cc_final: 0.8217 (m-30) REVERT: B 643 TYR cc_start: 0.8750 (m-10) cc_final: 0.8268 (m-80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2808 time to fit residues: 90.4162 Evaluate side-chains 154 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN D 658 GLN F 585 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16098 Z= 0.265 Angle : 0.629 9.402 21894 Z= 0.315 Chirality : 0.046 0.236 2793 Planarity : 0.004 0.045 2680 Dihedral : 7.677 59.350 3986 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1666 helix: 1.52 (0.27), residues: 395 sheet: -0.09 (0.25), residues: 399 loop : -0.68 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 45 HIS 0.014 0.001 HIS F 585 PHE 0.020 0.002 PHE E 53 TYR 0.019 0.002 TYR C 173 ARG 0.003 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 390 LEU cc_start: 0.9448 (mt) cc_final: 0.9205 (mt) REVERT: C 475 MET cc_start: 0.8687 (mmm) cc_final: 0.8469 (mmm) REVERT: C 486 TYR cc_start: 0.8730 (m-80) cc_final: 0.8379 (m-80) REVERT: D 577 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8712 (tm-30) REVERT: D 639 THR cc_start: 0.8488 (m) cc_final: 0.7413 (m) REVERT: D 643 TYR cc_start: 0.8587 (m-80) cc_final: 0.8300 (m-80) REVERT: D 652 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8554 (tp-100) REVERT: E 42 VAL cc_start: 0.8329 (t) cc_final: 0.7869 (m) REVERT: E 69 TRP cc_start: 0.9063 (m100) cc_final: 0.8109 (m-10) REVERT: E 95 MET cc_start: 0.8812 (ttp) cc_final: 0.8092 (tmm) REVERT: E 390 LEU cc_start: 0.9618 (mt) cc_final: 0.9244 (mt) REVERT: E 426 MET cc_start: 0.8506 (mtp) cc_final: 0.8223 (mtp) REVERT: E 434 MET cc_start: 0.9213 (ttp) cc_final: 0.8923 (ttp) REVERT: F 571 TRP cc_start: 0.8365 (t60) cc_final: 0.7885 (t60) REVERT: F 654 GLU cc_start: 0.8541 (tt0) cc_final: 0.8134 (tp30) REVERT: A 69 TRP cc_start: 0.8992 (m100) cc_final: 0.8422 (m-90) REVERT: A 131 CYS cc_start: 0.6301 (m) cc_final: 0.5874 (m) REVERT: A 161 MET cc_start: 0.8623 (ttt) cc_final: 0.8365 (ttt) REVERT: A 180 ASP cc_start: 0.8761 (m-30) cc_final: 0.8245 (m-30) REVERT: B 643 TYR cc_start: 0.8768 (m-10) cc_final: 0.8306 (m-80) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2898 time to fit residues: 87.5364 Evaluate side-chains 145 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 20.0000 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 40.0000 chunk 101 optimal weight: 0.0270 chunk 73 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN E 287 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16098 Z= 0.249 Angle : 0.635 12.421 21894 Z= 0.316 Chirality : 0.049 0.890 2793 Planarity : 0.004 0.075 2680 Dihedral : 7.667 67.047 3986 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1666 helix: 1.51 (0.27), residues: 396 sheet: -0.14 (0.25), residues: 397 loop : -0.71 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 45 HIS 0.007 0.001 HIS C 85 PHE 0.019 0.002 PHE E 53 TYR 0.018 0.002 TYR D 643 ARG 0.021 0.001 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8962 (tpp) cc_final: 0.8554 (tpp) REVERT: C 161 MET cc_start: 0.8991 (tpp) cc_final: 0.8775 (tpp) REVERT: C 390 LEU cc_start: 0.9431 (mt) cc_final: 0.9200 (mt) REVERT: D 577 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8722 (tm-30) REVERT: D 639 THR cc_start: 0.8461 (m) cc_final: 0.7258 (m) REVERT: D 643 TYR cc_start: 0.8591 (m-80) cc_final: 0.8268 (m-80) REVERT: D 656 ASN cc_start: 0.9085 (m-40) cc_final: 0.8734 (m110) REVERT: E 42 VAL cc_start: 0.8329 (t) cc_final: 0.7857 (m) REVERT: E 69 TRP cc_start: 0.9075 (m100) cc_final: 0.8106 (m-10) REVERT: E 95 MET cc_start: 0.8812 (ttp) cc_final: 0.8113 (tmm) REVERT: E 260 LEU cc_start: 0.9405 (mp) cc_final: 0.9199 (mp) REVERT: E 390 LEU cc_start: 0.9603 (mt) cc_final: 0.9235 (mt) REVERT: E 426 MET cc_start: 0.8509 (mtp) cc_final: 0.8183 (mtp) REVERT: E 434 MET cc_start: 0.9227 (ttp) cc_final: 0.8920 (ttp) REVERT: F 571 TRP cc_start: 0.8316 (t60) cc_final: 0.7835 (t60) REVERT: F 654 GLU cc_start: 0.8579 (tt0) cc_final: 0.8237 (pt0) REVERT: A 69 TRP cc_start: 0.8972 (m100) cc_final: 0.8384 (m-90) REVERT: A 131 CYS cc_start: 0.6248 (m) cc_final: 0.5815 (m) REVERT: A 180 ASP cc_start: 0.8768 (m-30) cc_final: 0.8246 (m-30) REVERT: B 599 SER cc_start: 0.9361 (p) cc_final: 0.9139 (p) REVERT: B 643 TYR cc_start: 0.8737 (m-10) cc_final: 0.8256 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2655 time to fit residues: 80.1317 Evaluate side-chains 149 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 149 optimal weight: 0.0010 chunk 15 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN E 203 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16098 Z= 0.261 Angle : 0.630 9.405 21894 Z= 0.316 Chirality : 0.046 0.385 2793 Planarity : 0.004 0.085 2680 Dihedral : 8.040 123.727 3986 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1666 helix: 1.63 (0.27), residues: 389 sheet: -0.19 (0.25), residues: 399 loop : -0.76 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 45 HIS 0.005 0.001 HIS C 85 PHE 0.020 0.002 PHE E 53 TYR 0.022 0.002 TYR C 486 ARG 0.020 0.001 ARG C 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 390 LEU cc_start: 0.9414 (mt) cc_final: 0.9197 (mt) REVERT: C 484 TYR cc_start: 0.8787 (p90) cc_final: 0.8572 (p90) REVERT: D 577 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8723 (tm-30) REVERT: D 643 TYR cc_start: 0.8612 (m-80) cc_final: 0.8302 (m-80) REVERT: E 42 VAL cc_start: 0.8361 (t) cc_final: 0.7942 (m) REVERT: E 69 TRP cc_start: 0.9082 (m100) cc_final: 0.8129 (m-10) REVERT: E 95 MET cc_start: 0.8854 (ttp) cc_final: 0.8191 (tmm) REVERT: E 390 LEU cc_start: 0.9602 (mt) cc_final: 0.9233 (mt) REVERT: E 426 MET cc_start: 0.8524 (mtp) cc_final: 0.8239 (mtp) REVERT: E 434 MET cc_start: 0.9222 (ttp) cc_final: 0.8948 (ttp) REVERT: F 571 TRP cc_start: 0.8320 (t60) cc_final: 0.7902 (t60) REVERT: F 654 GLU cc_start: 0.8615 (tt0) cc_final: 0.8257 (pt0) REVERT: A 69 TRP cc_start: 0.8979 (m100) cc_final: 0.8386 (m-90) REVERT: A 131 CYS cc_start: 0.6288 (m) cc_final: 0.5918 (m) REVERT: A 180 ASP cc_start: 0.8787 (m-30) cc_final: 0.8270 (m-30) REVERT: B 599 SER cc_start: 0.9348 (p) cc_final: 0.9123 (p) REVERT: B 643 TYR cc_start: 0.8832 (m-10) cc_final: 0.8387 (m-80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2977 time to fit residues: 88.1267 Evaluate side-chains 143 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 0.0870 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN E 203 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.073281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058859 restraints weight = 66064.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060337 restraints weight = 40452.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061375 restraints weight = 29400.910| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16098 Z= 0.231 Angle : 0.605 9.376 21894 Z= 0.305 Chirality : 0.045 0.332 2793 Planarity : 0.004 0.068 2680 Dihedral : 7.764 115.380 3986 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1666 helix: 1.70 (0.27), residues: 390 sheet: -0.21 (0.25), residues: 413 loop : -0.78 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 45 HIS 0.005 0.001 HIS C 249 PHE 0.018 0.002 PHE B 522 TYR 0.018 0.002 TYR D 643 ARG 0.018 0.001 ARG C 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.70 seconds wall clock time: 54 minutes 52.57 seconds (3292.57 seconds total)