Starting phenix.real_space_refine on Tue Apr 9 00:26:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/04_2024/8ejj_28184.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/04_2024/8ejj_28184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/04_2024/8ejj_28184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/04_2024/8ejj_28184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/04_2024/8ejj_28184.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/04_2024/8ejj_28184.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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 114 5.16 5 C 9276 2.51 5 N 2367 2.21 5 O 3105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 118": "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: 14862 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "I" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "J" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "a" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "b" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "c" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "h" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "l" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.17, per 1000 atoms: 0.55 Number of scatterers: 14862 At special positions: 0 Unit cell: (131.1, 129.95, 102.35, 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 114 16.00 O 3105 8.00 N 2367 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.15 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.15 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.15 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.15 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 111D" distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.02 Simple disulfide: pdb=" SG CYS I 110 " - pdb=" SG CYS I 111D" distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.02 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.01 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.01 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.01 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 104 " distance=2.02 Simple disulfide: pdb=" SG CYS h 110 " - pdb=" SG CYS h 111D" distance=2.02 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Z 4 " - " MAN Z 5 " " MAN f 4 " - " MAN f 5 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA D 3 " - " MAN l 201 " " BMA N 3 " - " MAN N 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " BMA N 3 " - " MAN N 5 " " BMA T 3 " - " MAN T 5 " " BMA Z 3 " - " MAN Z 6 " " BMA f 3 " - " MAN f 6 " " BMA j 3 " - " MAN j 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG m 1 " - " NAG m 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG B 301 " - " ASN B 99 " " NAG C 301 " - " ASN C 99 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 119 " " NAG K 1 " - " ASN A 167 " " NAG M 1 " - " ASN A 224 " " NAG N 1 " - " ASN B 79 " " NAG O 1 " - " ASN B 89 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 119 " " NAG R 1 " - " ASN B 167 " " NAG S 1 " - " ASN B 224 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 119 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN a 365 " " NAG a 501 " - " ASN a 395 " " NAG b 501 " - " ASN b 395 " " NAG c 501 " - " ASN c 395 " " NAG d 1 " - " ASN a 373 " " NAG e 1 " - " ASN a 390 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 373 " " NAG i 1 " - " ASN b 390 " " NAG j 1 " - " ASN c 365 " " NAG k 1 " - " ASN c 373 " " NAG m 1 " - " ASN c 390 " Time building additional restraints: 7.61 Conformation dependent library (CDL) restraints added in 2.6 seconds 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 27 sheets defined 27.9% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 removed outlier: 4.005A pdb=" N ILE A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 183 through 195 removed outlier: 4.215A pdb=" N GLN A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 removed outlier: 4.004A pdb=" N ILE B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 183 through 195 removed outlier: 4.214A pdb=" N GLN B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 removed outlier: 4.006A pdb=" N ILE C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 183 through 195 removed outlier: 4.215A pdb=" N GLN C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'H' and resid 71 through 74 No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'H' and resid 111A through 112 removed outlier: 3.640A pdb=" N CYS H 111D" --> pdb=" O SER H 111A" (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 74 No H-bonds generated for 'chain 'I' and resid 71 through 74' Processing helix chain 'I' and resid 111A through 112 removed outlier: 3.641A pdb=" N CYS I 111D" --> pdb=" O SER I 111A" (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU a 344 " --> pdb=" O ALA a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.929A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 423 Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU b 344 " --> pdb=" O ALA b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.930A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 423 Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU c 344 " --> pdb=" O ALA c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.929A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 423 Processing helix chain 'h' and resid 71 through 74 No H-bonds generated for 'chain 'h' and resid 71 through 74' Processing helix chain 'h' and resid 111A through 112 removed outlier: 3.641A pdb=" N CYS h 111D" --> pdb=" O SER h 111A" (cutoff:3.500A) Processing helix chain 'l' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 155 removed outlier: 4.507A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR A 87 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG A 235 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 155 removed outlier: 4.507A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B 87 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 235 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.507A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR C 87 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG C 235 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.105A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 19 through 22 Processing sheet with id=AA9, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.105A pdb=" N ARG I 43 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP I 52 " --> pdb=" O ARG I 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AB2, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.546A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.548A pdb=" N TRP L 41 " --> pdb=" O VAL L 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB8, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB9, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AC1, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AC2, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AC3, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AC4, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AC5, first strand: chain 'h' and resid 12 through 13 removed outlier: 6.106A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 19 through 22 Processing sheet with id=AC7, first strand: chain 'l' and resid 9 through 12 removed outlier: 6.548A pdb=" N TRP l 41 " --> pdb=" O VAL l 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'l' and resid 9 through 12 Processing sheet with id=AC9, first strand: chain 'l' and resid 19 through 24 579 hydrogen bonds defined for protein. 1449 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: 4.42 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3699 1.33 - 1.47: 5128 1.47 - 1.61: 6185 1.61 - 1.75: 37 1.75 - 1.90: 134 Bond restraints: 15183 Sorted by residual: bond pdb=" CB HIS b 354 " pdb=" CG HIS b 354 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.73e+01 bond pdb=" CB LEU l 127 " pdb=" CG LEU l 127 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" CB HIS a 354 " pdb=" CG HIS a 354 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" CB HIS A 141 " pdb=" CG HIS A 141 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.66e+01 bond pdb=" CB LEU L 127 " pdb=" CG LEU L 127 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 15178 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.20: 890 107.20 - 113.98: 8253 113.98 - 120.77: 6726 120.77 - 127.55: 4565 127.55 - 134.33: 173 Bond angle restraints: 20607 Sorted by residual: angle pdb=" N PRO H 45 " pdb=" CA PRO H 45 " pdb=" C PRO H 45 " ideal model delta sigma weight residual 110.47 102.96 7.51 9.60e-01 1.09e+00 6.12e+01 angle pdb=" N VAL H 76 " pdb=" CA VAL H 76 " pdb=" C VAL H 76 " ideal model delta sigma weight residual 108.11 118.92 -10.81 1.40e+00 5.10e-01 5.96e+01 angle pdb=" N PRO I 45 " pdb=" CA PRO I 45 " pdb=" C PRO I 45 " ideal model delta sigma weight residual 110.47 103.07 7.40 9.60e-01 1.09e+00 5.93e+01 angle pdb=" N PRO h 45 " pdb=" CA PRO h 45 " pdb=" C PRO h 45 " ideal model delta sigma weight residual 110.47 103.09 7.38 9.60e-01 1.09e+00 5.92e+01 angle pdb=" N VAL I 76 " pdb=" CA VAL I 76 " pdb=" C VAL I 76 " ideal model delta sigma weight residual 108.11 118.85 -10.74 1.40e+00 5.10e-01 5.88e+01 ... (remaining 20602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 9774 21.35 - 42.71: 225 42.71 - 64.06: 75 64.06 - 85.41: 54 85.41 - 106.77: 45 Dihedral angle restraints: 10173 sinusoidal: 5103 harmonic: 5070 Sorted by residual: dihedral pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.46 -59.54 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS A 180 " pdb=" SG CYS A 180 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.61 -59.39 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS C 180 " pdb=" SG CYS C 180 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.67 -59.33 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 10170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1552 0.103 - 0.206: 591 0.206 - 0.309: 225 0.309 - 0.412: 114 0.412 - 0.516: 38 Chirality restraints: 2520 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 BMA g 3 " pdb=" O4 NAG g 2 " pdb=" C2 BMA g 3 " pdb=" O5 BMA g 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 2517 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 89 " -0.056 2.00e-02 2.50e+03 5.76e-02 4.14e+01 pdb=" CG ASN C 89 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 89 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 89 " 0.088 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 89 " 0.056 2.00e-02 2.50e+03 5.74e-02 4.12e+01 pdb=" CG ASN B 89 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 89 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 89 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 89 " -0.056 2.00e-02 2.50e+03 5.72e-02 4.09e+01 pdb=" CG ASN A 89 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 89 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 89 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.069 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 5960 2.90 - 3.40: 13477 3.40 - 3.90: 25244 3.90 - 4.40: 29786 4.40 - 4.90: 47733 Nonbonded interactions: 122200 Sorted by model distance: nonbonded pdb=" OH TYR h 38 " pdb=" O CYS h 111D" model vdw 2.394 2.440 nonbonded pdb=" OH TYR H 38 " pdb=" O CYS H 111D" model vdw 2.394 2.440 nonbonded pdb=" OH TYR I 38 " pdb=" O CYS I 111D" model vdw 2.394 2.440 nonbonded pdb=" O4 MAN j 4 " pdb=" O6 MAN j 4 " model vdw 2.395 2.440 nonbonded pdb=" O4 MAN Z 4 " pdb=" O6 MAN Z 4 " model vdw 2.396 2.440 ... (remaining 122195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'e' selection = chain 'i' selection = chain 'm' } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'h' } ncs_group { reference = chain 'J' selection = chain 'L' selection = (chain 'l' and resid 2 through 127) } ncs_group { reference = chain 'N' selection = chain 'T' } ncs_group { reference = chain 'Z' selection = chain 'f' selection = chain 'j' } ncs_group { reference = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.860 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 42.550 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.024 0.138 15183 Z= 1.541 Angle : 1.797 11.893 20607 Z= 1.149 Chirality : 0.146 0.516 2520 Planarity : 0.009 0.079 2490 Dihedral : 13.946 106.765 6843 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.28 (0.20), residues: 1713 helix: -1.15 (0.23), residues: 369 sheet: 0.95 (0.26), residues: 450 loop : 0.56 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.010 TRP H 52 HIS 0.010 0.002 HIS c 354 PHE 0.030 0.007 PHE h 115 TYR 0.063 0.008 TYR H 26 ARG 0.009 0.001 ARG h 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8970 (mmp) cc_final: 0.8744 (mmt) REVERT: A 115 HIS cc_start: 0.7304 (m170) cc_final: 0.7102 (m90) REVERT: B 115 HIS cc_start: 0.7382 (m170) cc_final: 0.7135 (m-70) REVERT: J 67 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8495 (ttm110) REVERT: L 67 ARG cc_start: 0.8766 (ttp-110) cc_final: 0.8438 (ttm110) REVERT: c 332 MET cc_start: 0.8178 (tmt) cc_final: 0.7120 (tmt) REVERT: c 401 ASP cc_start: 0.7665 (m-30) cc_final: 0.7438 (m-30) REVERT: c 410 MET cc_start: 0.8516 (mtp) cc_final: 0.8222 (mtp) REVERT: c 419 TYR cc_start: 0.8216 (t80) cc_final: 0.7967 (t80) REVERT: l 18 THR cc_start: 0.8356 (m) cc_final: 0.8040 (p) REVERT: l 67 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8213 (ttm110) REVERT: l 123 LYS cc_start: 0.8313 (ttmm) cc_final: 0.8031 (ttmm) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3598 time to fit residues: 180.2052 Evaluate side-chains 197 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 58 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 324 GLN b 331 GLN ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN c 331 GLN h 58 HIS ** l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15183 Z= 0.269 Angle : 0.738 6.564 20607 Z= 0.376 Chirality : 0.049 0.247 2520 Planarity : 0.005 0.046 2490 Dihedral : 11.320 78.650 3657 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.88 % Allowed : 6.24 % Favored : 91.88 % 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: 0.66 (0.21), residues: 1713 helix: 0.38 (0.26), residues: 366 sheet: 1.06 (0.26), residues: 435 loop : 0.28 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 210 HIS 0.004 0.001 HIS c 305 PHE 0.018 0.002 PHE A 117 TYR 0.018 0.002 TYR b 419 ARG 0.005 0.001 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7384 (m170) cc_final: 0.7162 (m90) REVERT: A 122 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: A 204 ASP cc_start: 0.8330 (t0) cc_final: 0.8054 (t0) REVERT: B 115 HIS cc_start: 0.7426 (m170) cc_final: 0.7176 (m-70) REVERT: B 151 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: C 204 ASP cc_start: 0.8423 (t0) cc_final: 0.8058 (t0) REVERT: J 123 LYS cc_start: 0.8464 (tttt) cc_final: 0.8235 (mttp) REVERT: b 332 MET cc_start: 0.8192 (tmt) cc_final: 0.7804 (tmm) REVERT: b 333 SER cc_start: 0.8124 (t) cc_final: 0.7653 (p) REVERT: c 401 ASP cc_start: 0.7669 (m-30) cc_final: 0.7455 (m-30) REVERT: l 123 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8247 (mmtm) outliers start: 29 outliers final: 16 residues processed: 254 average time/residue: 0.3552 time to fit residues: 128.3812 Evaluate side-chains 220 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 15183 Z= 0.266 Angle : 0.673 7.001 20607 Z= 0.338 Chirality : 0.046 0.237 2520 Planarity : 0.005 0.042 2490 Dihedral : 9.420 71.751 3657 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.75 % Allowed : 7.99 % Favored : 90.25 % 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: 0.55 (0.21), residues: 1713 helix: 0.97 (0.28), residues: 372 sheet: 0.89 (0.25), residues: 438 loop : -0.09 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 210 HIS 0.011 0.002 HIS B 179 PHE 0.016 0.001 PHE A 117 TYR 0.017 0.001 TYR h 26 ARG 0.006 0.001 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7311 (m170) cc_final: 0.7071 (m90) REVERT: A 204 ASP cc_start: 0.8317 (t0) cc_final: 0.8003 (t0) REVERT: B 115 HIS cc_start: 0.7286 (m170) cc_final: 0.6894 (m90) REVERT: C 115 HIS cc_start: 0.7164 (m170) cc_final: 0.6953 (m90) REVERT: C 204 ASP cc_start: 0.8293 (t0) cc_final: 0.7993 (t0) REVERT: I 48 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8345 (mttm) REVERT: J 123 LYS cc_start: 0.8511 (tttt) cc_final: 0.8278 (mttp) REVERT: c 401 ASP cc_start: 0.7603 (m-30) cc_final: 0.7370 (m-30) REVERT: c 410 MET cc_start: 0.8191 (mtp) cc_final: 0.7989 (mtp) REVERT: h 29 SER cc_start: 0.8459 (m) cc_final: 0.8002 (t) REVERT: l 123 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8212 (mmtm) outliers start: 27 outliers final: 18 residues processed: 218 average time/residue: 0.2891 time to fit residues: 91.6092 Evaluate side-chains 193 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain a residue 283 TRP Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 101 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 0.0030 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 209 ASN C 93 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15183 Z= 0.214 Angle : 0.627 8.759 20607 Z= 0.311 Chirality : 0.045 0.237 2520 Planarity : 0.004 0.045 2490 Dihedral : 7.932 62.943 3657 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.21 % Allowed : 9.10 % Favored : 88.69 % 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: 0.53 (0.20), residues: 1713 helix: 1.27 (0.28), residues: 369 sheet: 0.84 (0.24), residues: 441 loop : -0.23 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 210 HIS 0.003 0.001 HIS B 230 PHE 0.013 0.001 PHE A 117 TYR 0.016 0.001 TYR b 419 ARG 0.005 0.001 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7238 (m170) cc_final: 0.6991 (m90) REVERT: A 204 ASP cc_start: 0.8281 (t0) cc_final: 0.7954 (t0) REVERT: B 115 HIS cc_start: 0.7234 (m170) cc_final: 0.6861 (m90) REVERT: C 204 ASP cc_start: 0.8333 (t0) cc_final: 0.8043 (t0) REVERT: I 48 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8469 (mttm) REVERT: I 85 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7793 (t0) REVERT: J 123 LYS cc_start: 0.8483 (tttt) cc_final: 0.8276 (mttp) REVERT: L 101 ASP cc_start: 0.7753 (m-30) cc_final: 0.7481 (m-30) REVERT: L 123 LYS cc_start: 0.8055 (mptt) cc_final: 0.7727 (mmtm) REVERT: c 324 GLN cc_start: 0.8701 (mt0) cc_final: 0.8424 (mt0) REVERT: c 410 MET cc_start: 0.8170 (mtp) cc_final: 0.7841 (mtp) REVERT: h 29 SER cc_start: 0.8351 (m) cc_final: 0.7989 (t) REVERT: h 94 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8790 (p) REVERT: l 123 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8140 (mmtm) outliers start: 34 outliers final: 26 residues processed: 216 average time/residue: 0.2797 time to fit residues: 88.9303 Evaluate side-chains 211 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 0.0670 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 209 ASN B 189 GLN C 185 ASN H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15183 Z= 0.236 Angle : 0.610 5.927 20607 Z= 0.301 Chirality : 0.044 0.217 2520 Planarity : 0.004 0.046 2490 Dihedral : 7.277 58.051 3657 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.60 % Allowed : 9.68 % Favored : 87.72 % 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: 1713 helix: 1.37 (0.28), residues: 369 sheet: 1.13 (0.25), residues: 417 loop : -0.44 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 210 HIS 0.004 0.001 HIS B 230 PHE 0.013 0.001 PHE A 117 TYR 0.015 0.001 TYR b 419 ARG 0.006 0.001 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7140 (m170) cc_final: 0.6889 (m90) REVERT: A 204 ASP cc_start: 0.8249 (t0) cc_final: 0.7887 (t0) REVERT: B 115 HIS cc_start: 0.7199 (m170) cc_final: 0.6903 (m90) REVERT: C 204 ASP cc_start: 0.8430 (t0) cc_final: 0.8204 (t0) REVERT: I 48 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8499 (mttm) REVERT: I 85 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7968 (t0) REVERT: J 123 LYS cc_start: 0.8471 (tttt) cc_final: 0.8262 (mttp) REVERT: L 123 LYS cc_start: 0.8117 (mptt) cc_final: 0.7745 (mmtm) REVERT: b 356 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8158 (mtt180) REVERT: c 324 GLN cc_start: 0.8718 (mt0) cc_final: 0.8440 (mt0) REVERT: c 332 MET cc_start: 0.8299 (tmt) cc_final: 0.7609 (tmt) REVERT: c 410 MET cc_start: 0.8198 (mtp) cc_final: 0.7587 (mtp) REVERT: h 94 VAL cc_start: 0.9087 (p) cc_final: 0.8831 (p) REVERT: l 123 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8116 (mmtm) outliers start: 40 outliers final: 33 residues processed: 212 average time/residue: 0.3003 time to fit residues: 94.0906 Evaluate side-chains 218 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 101 ASP Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.132 15183 Z= 0.505 Angle : 0.743 8.559 20607 Z= 0.367 Chirality : 0.050 0.226 2520 Planarity : 0.005 0.056 2490 Dihedral : 7.424 57.562 3657 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.18 % Allowed : 9.68 % Favored : 87.13 % 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: 1713 helix: 1.03 (0.27), residues: 372 sheet: 0.79 (0.25), residues: 402 loop : -0.75 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 210 HIS 0.008 0.002 HIS B 141 PHE 0.028 0.002 PHE A 117 TYR 0.013 0.002 TYR B 62 ARG 0.006 0.001 ARG H 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 183 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7446 (m170) cc_final: 0.7164 (m90) REVERT: A 204 ASP cc_start: 0.8334 (t0) cc_final: 0.8036 (t0) REVERT: B 115 HIS cc_start: 0.7644 (m170) cc_final: 0.7255 (m90) REVERT: I 48 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8620 (mttp) REVERT: L 123 LYS cc_start: 0.8183 (mptt) cc_final: 0.7851 (mmtm) REVERT: c 332 MET cc_start: 0.8151 (tmt) cc_final: 0.7496 (tmt) REVERT: c 410 MET cc_start: 0.8330 (mtp) cc_final: 0.7671 (mtp) REVERT: h 94 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8948 (p) REVERT: l 123 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8028 (mmtm) outliers start: 49 outliers final: 39 residues processed: 216 average time/residue: 0.2863 time to fit residues: 91.6608 Evaluate side-chains 219 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 298 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 101 ASP Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 218 GLN C 185 ASN C 189 GLN H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15183 Z= 0.203 Angle : 0.615 7.907 20607 Z= 0.304 Chirality : 0.044 0.221 2520 Planarity : 0.004 0.051 2490 Dihedral : 6.903 59.673 3657 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.73 % Allowed : 10.14 % Favored : 87.13 % 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: 0.18 (0.20), residues: 1713 helix: 1.38 (0.28), residues: 369 sheet: 0.95 (0.26), residues: 387 loop : -0.76 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 210 HIS 0.003 0.001 HIS C 230 PHE 0.011 0.001 PHE A 117 TYR 0.010 0.001 TYR H 26 ARG 0.006 0.000 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7095 (m170) cc_final: 0.6860 (m90) REVERT: A 204 ASP cc_start: 0.8299 (t0) cc_final: 0.7982 (t0) REVERT: B 115 HIS cc_start: 0.7412 (m170) cc_final: 0.7099 (m90) REVERT: I 48 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8572 (mttm) REVERT: I 85 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7949 (t0) REVERT: L 123 LYS cc_start: 0.8220 (mptt) cc_final: 0.7999 (mmtm) REVERT: c 332 MET cc_start: 0.8097 (tmt) cc_final: 0.7531 (tmt) REVERT: c 410 MET cc_start: 0.8277 (mtp) cc_final: 0.7623 (mtp) REVERT: h 94 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8875 (p) REVERT: l 123 LYS cc_start: 0.8360 (ttmm) cc_final: 0.8021 (mmtm) outliers start: 42 outliers final: 36 residues processed: 214 average time/residue: 0.2733 time to fit residues: 86.7271 Evaluate side-chains 220 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 101 ASP Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 218 GLN B 218 GLN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 15183 Z= 0.269 Angle : 0.629 8.473 20607 Z= 0.309 Chirality : 0.044 0.213 2520 Planarity : 0.005 0.051 2490 Dihedral : 6.781 58.577 3657 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.79 % Allowed : 9.94 % Favored : 87.26 % 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: 0.13 (0.20), residues: 1713 helix: 1.36 (0.28), residues: 372 sheet: 0.83 (0.27), residues: 363 loop : -0.72 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 210 HIS 0.004 0.001 HIS B 141 PHE 0.014 0.001 PHE A 117 TYR 0.010 0.001 TYR L 55 ARG 0.007 0.000 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7134 (m170) cc_final: 0.6863 (m90) REVERT: A 204 ASP cc_start: 0.8336 (t0) cc_final: 0.8004 (t0) REVERT: B 115 HIS cc_start: 0.7438 (m170) cc_final: 0.7109 (m90) REVERT: I 48 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8584 (mttm) REVERT: L 123 LYS cc_start: 0.8222 (mptt) cc_final: 0.7995 (mmtm) REVERT: b 420 MET cc_start: 0.8328 (mmp) cc_final: 0.7764 (tmm) REVERT: c 332 MET cc_start: 0.8092 (tmt) cc_final: 0.7640 (tmt) REVERT: c 410 MET cc_start: 0.8298 (mtp) cc_final: 0.7632 (mtp) REVERT: h 94 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8871 (p) REVERT: l 123 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8021 (mmtm) outliers start: 43 outliers final: 38 residues processed: 211 average time/residue: 0.2621 time to fit residues: 81.9147 Evaluate side-chains 216 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 101 ASP Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 0.0980 chunk 136 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 218 GLN C 115 HIS C 185 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 ASN ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15183 Z= 0.174 Angle : 0.593 8.487 20607 Z= 0.291 Chirality : 0.043 0.215 2520 Planarity : 0.004 0.049 2490 Dihedral : 6.488 57.800 3657 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.34 % Allowed : 10.33 % Favored : 87.33 % 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: 0.20 (0.20), residues: 1713 helix: 1.58 (0.28), residues: 369 sheet: 0.73 (0.27), residues: 369 loop : -0.69 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 210 HIS 0.003 0.001 HIS A 230 PHE 0.009 0.001 PHE A 117 TYR 0.009 0.001 TYR l 55 ARG 0.007 0.000 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6976 (m170) cc_final: 0.6730 (m90) REVERT: A 204 ASP cc_start: 0.8282 (t0) cc_final: 0.7950 (t0) REVERT: B 115 HIS cc_start: 0.7252 (m170) cc_final: 0.6957 (m90) REVERT: L 123 LYS cc_start: 0.8241 (mptt) cc_final: 0.8015 (mmtm) REVERT: b 420 MET cc_start: 0.8378 (mmp) cc_final: 0.7732 (tmm) REVERT: c 332 MET cc_start: 0.8102 (tmt) cc_final: 0.7699 (tmt) REVERT: h 94 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8698 (p) REVERT: l 123 LYS cc_start: 0.8363 (ttmm) cc_final: 0.8028 (mmtm) outliers start: 36 outliers final: 34 residues processed: 216 average time/residue: 0.3067 time to fit residues: 97.9666 Evaluate side-chains 216 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 0.0070 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 141 optimal weight: 0.7980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 218 GLN C 185 ASN C 218 GLN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15183 Z= 0.194 Angle : 0.598 9.762 20607 Z= 0.294 Chirality : 0.043 0.301 2520 Planarity : 0.004 0.049 2490 Dihedral : 6.360 57.515 3657 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.40 % Allowed : 10.59 % Favored : 87.00 % 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: 0.18 (0.20), residues: 1713 helix: 1.57 (0.28), residues: 369 sheet: 0.73 (0.27), residues: 369 loop : -0.70 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 210 HIS 0.009 0.001 HIS C 115 PHE 0.010 0.001 PHE A 117 TYR 0.010 0.001 TYR l 55 ARG 0.007 0.000 ARG c 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6935 (m170) cc_final: 0.6714 (m90) REVERT: A 204 ASP cc_start: 0.8310 (t0) cc_final: 0.7981 (t0) REVERT: B 115 HIS cc_start: 0.7265 (m170) cc_final: 0.6961 (m90) REVERT: b 420 MET cc_start: 0.8396 (mmp) cc_final: 0.7726 (tmm) REVERT: c 332 MET cc_start: 0.8145 (tmt) cc_final: 0.7795 (tmt) REVERT: c 420 MET cc_start: 0.8466 (mmp) cc_final: 0.7963 (tmm) REVERT: l 123 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8032 (mttm) outliers start: 37 outliers final: 31 residues processed: 207 average time/residue: 0.2771 time to fit residues: 84.5847 Evaluate side-chains 209 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 218 GLN C 218 GLN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.093189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074862 restraints weight = 27855.128| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.60 r_work: 0.3012 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 15183 Z= 0.288 Angle : 0.634 7.893 20607 Z= 0.312 Chirality : 0.045 0.289 2520 Planarity : 0.005 0.054 2490 Dihedral : 6.397 58.503 3657 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.34 % Allowed : 10.92 % Favored : 86.74 % 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: 1713 helix: 1.41 (0.27), residues: 372 sheet: 0.63 (0.27), residues: 369 loop : -0.79 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 210 HIS 0.010 0.001 HIS C 115 PHE 0.016 0.001 PHE A 117 TYR 0.011 0.001 TYR H 38 ARG 0.007 0.001 ARG c 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3415.43 seconds wall clock time: 66 minutes 23.25 seconds (3983.25 seconds total)