Starting phenix.real_space_refine on Tue Aug 6 01:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/08_2024/8ejj_28184.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/08_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_28184/08_2024/8ejj_28184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/08_2024/8ejj_28184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/08_2024/8ejj_28184.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejj_28184/08_2024/8ejj_28184.cif" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 9.19, per 1000 atoms: 0.62 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: 7.79 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: 2.69 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: 6.35 Time building geometry restraints manager: 7.91 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 3.040 nonbonded pdb=" OH TYR H 38 " pdb=" O CYS H 111D" model vdw 2.394 3.040 nonbonded pdb=" OH TYR I 38 " pdb=" O CYS I 111D" model vdw 2.394 3.040 nonbonded pdb=" O4 MAN j 4 " pdb=" O6 MAN j 4 " model vdw 2.395 3.040 nonbonded pdb=" O4 MAN Z 4 " pdb=" O6 MAN Z 4 " model vdw 2.396 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.370 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 46.250 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.020 ------------------------------------------------------------------------------- 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 : 1.687 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: 0.3440 time to fit residues: 172.1766 Evaluate side-chains 197 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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: 0.7980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** 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 ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN h 58 HIS ** l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2608 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= 0.289 Angle : 0.755 6.451 20607 Z= 0.388 Chirality : 0.049 0.259 2520 Planarity : 0.005 0.045 2490 Dihedral : 11.455 79.975 3657 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.43 % Allowed : 6.63 % Favored : 91.94 % 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: 0.32 (0.26), residues: 366 sheet: 1.04 (0.26), residues: 432 loop : 0.32 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 210 HIS 0.004 0.001 HIS c 305 PHE 0.020 0.002 PHE A 117 TYR 0.017 0.002 TYR H 26 ARG 0.006 0.001 ARG b 282 *********************** 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 270 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7383 (m170) cc_final: 0.7148 (m90) REVERT: A 122 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: A 204 ASP cc_start: 0.8326 (t0) cc_final: 0.8056 (t0) REVERT: B 115 HIS cc_start: 0.7409 (m170) cc_final: 0.7033 (m90) REVERT: B 151 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: C 204 ASP cc_start: 0.8404 (t0) cc_final: 0.8038 (t0) REVERT: C 211 ASP cc_start: 0.6789 (p0) cc_final: 0.6368 (p0) REVERT: J 123 LYS cc_start: 0.8459 (tttt) cc_final: 0.8239 (mttp) REVERT: L 67 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8348 (ttm110) REVERT: b 332 MET cc_start: 0.8204 (tmt) cc_final: 0.7804 (tmm) REVERT: b 333 SER cc_start: 0.8079 (t) cc_final: 0.7618 (p) REVERT: c 401 ASP cc_start: 0.7653 (m-30) cc_final: 0.7452 (m-30) REVERT: l 123 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8223 (mmtm) outliers start: 22 outliers final: 12 residues processed: 254 average time/residue: 0.3089 time to fit residues: 110.0195 Evaluate side-chains 212 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 198 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 122 ASP 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 b residue 283 TRP 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: 3.9990 chunk 47 optimal weight: 0.0770 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 122 optimal weight: 0.4980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 15183 Z= 0.266 Angle : 0.684 7.235 20607 Z= 0.344 Chirality : 0.047 0.237 2520 Planarity : 0.005 0.042 2490 Dihedral : 9.514 72.069 3657 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 8.12 % Favored : 90.19 % 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: 0.52 (0.20), residues: 1713 helix: 0.94 (0.27), residues: 372 sheet: 0.94 (0.25), residues: 441 loop : -0.14 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 210 HIS 0.011 0.001 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 b 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 225 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7354 (m170) cc_final: 0.7102 (m90) REVERT: A 204 ASP cc_start: 0.8316 (t0) cc_final: 0.8014 (t0) REVERT: B 115 HIS cc_start: 0.7313 (m170) cc_final: 0.6927 (m90) REVERT: C 204 ASP cc_start: 0.8275 (t0) cc_final: 0.7983 (t0) REVERT: I 48 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8335 (mttm) REVERT: L 123 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7891 (mmtm) REVERT: c 401 ASP cc_start: 0.7613 (m-30) cc_final: 0.7373 (m-30) REVERT: c 410 MET cc_start: 0.8180 (mtp) cc_final: 0.7973 (mtp) REVERT: h 29 SER cc_start: 0.8437 (m) cc_final: 0.8044 (t) REVERT: l 123 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8236 (mmtm) outliers start: 26 outliers final: 18 residues processed: 213 average time/residue: 0.2963 time to fit residues: 90.8471 Evaluate side-chains 194 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 H residue 82 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain a residue 283 TRP Chi-restraints excluded: chain a residue 360 CYS 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 82 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15183 Z= 0.229 Angle : 0.642 8.491 20607 Z= 0.319 Chirality : 0.046 0.232 2520 Planarity : 0.004 0.045 2490 Dihedral : 8.021 62.776 3657 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.21 % Allowed : 8.84 % Favored : 88.95 % 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: 0.39 (0.20), residues: 1713 helix: 1.13 (0.27), residues: 372 sheet: 0.86 (0.25), residues: 435 loop : -0.37 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 210 HIS 0.006 0.001 HIS B 179 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 225 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7141 (m170) cc_final: 0.6897 (m90) REVERT: A 204 ASP cc_start: 0.8374 (t0) cc_final: 0.8048 (t0) REVERT: B 115 HIS cc_start: 0.7289 (m170) cc_final: 0.6905 (m90) REVERT: C 204 ASP cc_start: 0.8290 (t0) cc_final: 0.8023 (t0) REVERT: I 48 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8467 (mttm) REVERT: I 85 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7759 (t0) REVERT: c 324 GLN cc_start: 0.8738 (mt0) cc_final: 0.8450 (mt0) REVERT: c 410 MET cc_start: 0.8169 (mtp) cc_final: 0.7830 (mtp) REVERT: h 94 VAL cc_start: 0.9042 (p) cc_final: 0.8776 (p) REVERT: l 123 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8243 (mmtm) outliers start: 34 outliers final: 25 residues processed: 214 average time/residue: 0.2983 time to fit residues: 95.6875 Evaluate side-chains 200 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 B residue 180 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 180 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 71 LEU 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 51 VAL Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 284 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS C 185 ASN ** H 66 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** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 15183 Z= 0.368 Angle : 0.694 9.417 20607 Z= 0.344 Chirality : 0.048 0.232 2520 Planarity : 0.005 0.049 2490 Dihedral : 7.469 56.212 3657 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.34 % Allowed : 10.07 % Favored : 87.59 % 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: 0.23 (0.20), residues: 1713 helix: 1.10 (0.27), residues: 372 sheet: 1.05 (0.26), residues: 396 loop : -0.63 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 210 HIS 0.006 0.001 HIS B 141 PHE 0.022 0.002 PHE A 117 TYR 0.016 0.002 TYR b 419 ARG 0.006 0.001 ARG b 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 220 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7334 (m170) cc_final: 0.7047 (m90) REVERT: A 204 ASP cc_start: 0.8330 (t0) cc_final: 0.7962 (t0) REVERT: B 115 HIS cc_start: 0.7430 (m170) cc_final: 0.7066 (m90) REVERT: I 48 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8666 (mttm) REVERT: c 332 MET cc_start: 0.8215 (tmt) cc_final: 0.7578 (tmt) REVERT: c 410 MET cc_start: 0.8260 (mtp) cc_final: 0.7629 (mtp) REVERT: h 94 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8898 (p) REVERT: l 123 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8129 (mttm) outliers start: 36 outliers final: 28 residues processed: 208 average time/residue: 0.2838 time to fit residues: 85.9919 Evaluate side-chains 206 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU 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 a residue 284 MET Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** H 66 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** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15183 Z= 0.196 Angle : 0.610 6.434 20607 Z= 0.301 Chirality : 0.044 0.226 2520 Planarity : 0.004 0.048 2490 Dihedral : 6.954 55.728 3657 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.73 % Allowed : 10.53 % 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: 0.18 (0.20), residues: 1713 helix: 1.34 (0.27), residues: 369 sheet: 0.61 (0.25), residues: 441 loop : -0.63 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 210 HIS 0.003 0.001 HIS B 179 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 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 224 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 182 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7075 (m170) cc_final: 0.6797 (m90) REVERT: A 204 ASP cc_start: 0.8319 (t0) cc_final: 0.7932 (t0) REVERT: B 115 HIS cc_start: 0.7306 (m170) cc_final: 0.6971 (m90) REVERT: I 48 LYS cc_start: 0.8895 (mmtm) cc_final: 0.8678 (mttm) REVERT: b 356 ARG cc_start: 0.8636 (mtt180) cc_final: 0.8244 (mtt180) REVERT: c 332 MET cc_start: 0.8275 (tmt) cc_final: 0.7672 (tmt) REVERT: h 94 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8782 (p) REVERT: l 123 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8141 (mttm) outliers start: 42 outliers final: 30 residues processed: 210 average time/residue: 0.2758 time to fit residues: 85.8990 Evaluate side-chains 206 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 180 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 71 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS 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 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 127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 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** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15183 Z= 0.244 Angle : 0.629 7.271 20607 Z= 0.310 Chirality : 0.045 0.425 2520 Planarity : 0.005 0.048 2490 Dihedral : 6.769 57.895 3657 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.27 % Allowed : 10.79 % Favored : 86.94 % 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: 0.15 (0.20), residues: 1713 helix: 1.42 (0.27), residues: 369 sheet: 0.48 (0.25), residues: 417 loop : -0.61 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 210 HIS 0.004 0.001 HIS B 141 PHE 0.013 0.001 PHE A 117 TYR 0.011 0.001 TYR h 38 ARG 0.007 0.001 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 213 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7046 (m170) cc_final: 0.6774 (m90) REVERT: A 204 ASP cc_start: 0.8329 (t0) cc_final: 0.8016 (t0) REVERT: B 115 HIS cc_start: 0.7352 (m170) cc_final: 0.6977 (m90) REVERT: I 48 LYS cc_start: 0.8902 (mmtm) cc_final: 0.8684 (mttm) REVERT: b 356 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8228 (mtt180) REVERT: c 332 MET cc_start: 0.8240 (tmt) cc_final: 0.7766 (tmt) REVERT: c 410 MET cc_start: 0.8432 (mtp) cc_final: 0.7918 (mtp) REVERT: h 94 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8761 (p) REVERT: l 123 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8134 (mttm) outliers start: 35 outliers final: 30 residues processed: 200 average time/residue: 0.2906 time to fit residues: 84.8924 Evaluate side-chains 206 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 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 71 LEU 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 a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET 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 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 127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.0070 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15183 Z= 0.212 Angle : 0.615 7.977 20607 Z= 0.303 Chirality : 0.044 0.225 2520 Planarity : 0.005 0.049 2490 Dihedral : 6.567 59.892 3657 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.34 % Allowed : 10.53 % 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: 0.21 (0.20), residues: 1713 helix: 1.50 (0.28), residues: 369 sheet: 0.72 (0.26), residues: 384 loop : -0.64 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 210 HIS 0.004 0.001 HIS B 230 PHE 0.012 0.001 PHE A 117 TYR 0.011 0.001 TYR L 55 ARG 0.008 0.001 ARG b 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 216 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6966 (m170) cc_final: 0.6710 (m90) REVERT: A 204 ASP cc_start: 0.8351 (t0) cc_final: 0.8028 (t0) REVERT: B 115 HIS cc_start: 0.7445 (m170) cc_final: 0.7086 (m90) REVERT: b 356 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8173 (mtt180) REVERT: b 420 MET cc_start: 0.8264 (mmp) cc_final: 0.7725 (tmm) REVERT: c 332 MET cc_start: 0.8176 (tmt) cc_final: 0.7763 (tmt) REVERT: c 401 ASP cc_start: 0.7492 (m-30) cc_final: 0.6899 (m-30) REVERT: l 123 LYS cc_start: 0.8365 (ttmm) cc_final: 0.8139 (mttm) outliers start: 36 outliers final: 30 residues processed: 205 average time/residue: 0.2652 time to fit residues: 80.4647 Evaluate side-chains 207 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 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 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET 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 h residue 82 THR 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 127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 0.0270 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** b 353 ASN ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15183 Z= 0.214 Angle : 0.611 7.608 20607 Z= 0.301 Chirality : 0.044 0.208 2520 Planarity : 0.005 0.054 2490 Dihedral : 6.359 59.461 3657 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.21 % Allowed : 10.72 % Favored : 87.07 % 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: 0.16 (0.20), residues: 1713 helix: 1.43 (0.27), residues: 369 sheet: 0.81 (0.27), residues: 372 loop : -0.71 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 210 HIS 0.003 0.001 HIS A 141 PHE 0.012 0.001 PHE A 117 TYR 0.011 0.001 TYR L 55 ARG 0.008 0.001 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 220 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8336 (t0) cc_final: 0.8011 (t0) REVERT: B 115 HIS cc_start: 0.7356 (m170) cc_final: 0.7008 (m90) REVERT: C 151 GLU cc_start: 0.7955 (pt0) cc_final: 0.7653 (pm20) REVERT: b 356 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8203 (mtt180) REVERT: b 420 MET cc_start: 0.8348 (mmp) cc_final: 0.7709 (tmm) REVERT: c 332 MET cc_start: 0.8168 (tmt) cc_final: 0.7756 (tmt) REVERT: c 379 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.8066 (mtp85) REVERT: c 420 MET cc_start: 0.8429 (mmp) cc_final: 0.7915 (tmm) REVERT: l 123 LYS cc_start: 0.8358 (ttmm) cc_final: 0.8076 (mttm) outliers start: 34 outliers final: 27 residues processed: 211 average time/residue: 0.2778 time to fit residues: 85.6213 Evaluate side-chains 206 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 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 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET 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 h residue 82 THR 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 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** b 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 15183 Z= 0.309 Angle : 0.653 8.381 20607 Z= 0.321 Chirality : 0.046 0.205 2520 Planarity : 0.005 0.057 2490 Dihedral : 6.434 56.316 3657 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.95 % Allowed : 11.37 % Favored : 86.68 % 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: 0.05 (0.20), residues: 1713 helix: 1.35 (0.27), residues: 369 sheet: 0.79 (0.26), residues: 402 loop : -0.87 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 210 HIS 0.004 0.001 HIS C 141 PHE 0.019 0.001 PHE A 117 TYR 0.013 0.001 TYR h 38 ARG 0.007 0.001 ARG a 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 210 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8112 (pt0) cc_final: 0.7845 (pm20) REVERT: A 204 ASP cc_start: 0.8381 (t0) cc_final: 0.8026 (t0) REVERT: C 151 GLU cc_start: 0.7981 (pt0) cc_final: 0.7700 (pm20) REVERT: b 356 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8279 (mtt180) REVERT: c 332 MET cc_start: 0.8185 (tmt) cc_final: 0.7739 (tmt) REVERT: l 123 LYS cc_start: 0.8389 (ttmm) cc_final: 0.8078 (mttm) outliers start: 30 outliers final: 30 residues processed: 203 average time/residue: 0.2756 time to fit residues: 82.1722 Evaluate side-chains 203 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 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 85 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET 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 h residue 82 THR 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 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 64, in __init__ weight = self.w, xray_structure = self.xray_structure) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.6812 > 50: distance: 1642 - 1664: 3.030 distance: 2909 - 2938: 3.005 distance: 3360 - 3361: 3.138 distance: 3364 - 3366: 3.010 distance: 3969 - 3990: 3.197 distance: 3976 - 3997: 3.002 distance: 4165 - 4166: 4.302 distance: 4167 - 4169: 3.515 distance: 4168 - 4170: 3.132 distance: 4169 - 4170: 4.101 distance: 5025 - 5066: 3.503 distance: 5028 - 5063: 13.544 distance: 5047 - 5048: 7.597 distance: 5048 - 5049: 8.399 distance: 5048 - 5055: 21.664 distance: 5055 - 5056: 28.224 distance: 5056 - 5057: 25.230 distance: 5056 - 5059: 52.459 distance: 5057 - 5058: 34.199 distance: 5057 - 5063: 30.933 distance: 5059 - 5060: 56.681 distance: 5060 - 5061: 38.572 distance: 5060 - 5062: 48.363 distance: 5063 - 5064: 7.280 distance: 5064 - 5065: 10.657 distance: 5064 - 5067: 10.695 distance: 5067 - 5068: 6.828 distance: 7047 - 7117: 3.027 distance: 7856 - 7926: 3.014 distance: 8157 - 8186: 3.010 distance: 9173 - 9201: 3.036 distance: 9834 - 9864: 5.021 distance: 9855 - 9864: 3.259 distance: 9865 - 9868: 9.439 distance: 9868 - 9869: 7.343 distance: 9869 - 9871: 15.466 distance: 10773 - 10775: 3.144 distance: 11948 - 11983: 3.007 distance: 11957 - 11994: 3.046 distance: 13586 - 13656: 3.049