Starting phenix.real_space_refine on Fri Mar 15 16:15:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/03_2024/7sgf_25109.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/03_2024/7sgf_25109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/03_2024/7sgf_25109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/03_2024/7sgf_25109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/03_2024/7sgf_25109.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/03_2024/7sgf_25109.pdb" } resolution = 4.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 90 5.16 5 C 7404 2.51 5 N 2031 2.21 5 O 2553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12078 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "a" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "L" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "b" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "J" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "K" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "c" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "M" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "N" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 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: 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: "G" 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: "I" 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "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: 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "Z" 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: "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: 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: "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: 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: "h" 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: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "l" 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: "m" 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.15, per 1000 atoms: 0.51 Number of scatterers: 12078 At special positions: 0 Unit cell: (143.17, 135.96, 95.79, 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 90 16.00 O 2553 8.00 N 2031 7.00 C 7404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.08 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.01 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.08 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.01 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.08 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.01 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.04 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA U 3 " - " MAN U 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA U 3 " - " MAN U 5 " " BMA g 3 " - " MAN g 5 " 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " BETA1-6 " NAG P 1 " - " FUC P 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG Y 1 " - " FUC Y 4 " " NAG Z 1 " - " FUC Z 3 " " NAG k 1 " - " FUC k 4 " " NAG l 1 " - " FUC l 3 " NAG-ASN " NAG A 701 " - " ASN A 99 " " NAG A 702 " - " ASN A 224 " " NAG B 701 " - " ASN B 99 " " NAG B 702 " - " ASN B 224 " " NAG C 701 " - " ASN C 99 " " NAG C 702 " - " ASN C 224 " " 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 I 1 " - " ASN A 167 " " NAG O 1 " - " ASN a 373 " " NAG P 1 " - " ASN a 390 " " NAG Q 1 " - " ASN a 395 " " NAG R 1 " - " ASN a 365 " " NAG S 1 " - " ASN B 79 " " NAG T 1 " - " ASN B 89 " " NAG U 1 " - " ASN B 109 " " NAG V 1 " - " ASN B 119 " " NAG W 1 " - " ASN B 167 " " NAG X 1 " - " ASN b 373 " " NAG Y 1 " - " ASN b 390 " " NAG Z 1 " - " ASN b 395 " " NAG d 1 " - " ASN b 365 " " NAG e 1 " - " ASN C 79 " " NAG f 1 " - " ASN C 89 " " NAG g 1 " - " ASN C 109 " " NAG h 1 " - " ASN C 119 " " NAG i 1 " - " ASN C 167 " " NAG j 1 " - " ASN c 373 " " NAG k 1 " - " ASN c 390 " " NAG l 1 " - " ASN c 395 " " NAG m 1 " - " ASN c 365 " Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.3 seconds 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 27 sheets defined 23.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.539A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 415 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP H 67 " --> pdb=" O TRP H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'b' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.538A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 415 Processing helix chain 'J' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP J 67 " --> pdb=" O TRP J 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 64 through 67' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'c' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 345 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.538A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 415 Processing helix chain 'M' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP M 67 " --> pdb=" O TRP M 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 64 through 67' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 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 61 through 62 removed outlier: 4.441A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY H 16 " --> pdb=" O GLY H 85 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR H 78 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR H 74 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR H 80 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER H 72 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN H 82 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.287A pdb=" N CYS H 96 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP H 116 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS H 98 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.567A pdb=" N ARG H 109 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL L 11 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN b 365 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP b 386 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER b 367 " --> pdb=" O LYS b 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS b 384 " --> pdb=" O SER b 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AB4, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY J 16 " --> pdb=" O GLY J 85 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR J 78 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR J 74 " --> pdb=" O THR J 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR J 80 " --> pdb=" O SER J 72 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER J 72 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN J 82 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG J 39 " --> pdb=" O TRP J 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.287A pdb=" N CYS J 96 " --> pdb=" O TRP J 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP J 116 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS J 98 " --> pdb=" O ASP J 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 102 through 103 removed outlier: 3.567A pdb=" N ARG J 109 " --> pdb=" O ARG J 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL K 11 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AC2, first strand: chain 'C' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN c 365 " --> pdb=" O TRP c 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP c 386 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER c 367 " --> pdb=" O LYS c 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS c 384 " --> pdb=" O SER c 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AC4, first strand: chain 'M' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY M 16 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR M 78 " --> pdb=" O THR M 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR M 74 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR M 80 " --> pdb=" O SER M 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER M 72 " --> pdb=" O THR M 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN M 82 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG M 39 " --> pdb=" O TRP M 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP M 48 " --> pdb=" O ARG M 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.286A pdb=" N CYS M 96 " --> pdb=" O TRP M 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP M 116 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS M 98 " --> pdb=" O ASP M 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 102 through 103 removed outlier: 3.568A pdb=" N ARG M 109 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL N 11 " --> pdb=" O VAL N 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 5.98 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: 3101 1.33 - 1.47: 3750 1.47 - 1.60: 5224 1.60 - 1.74: 24 1.74 - 1.88: 132 Bond restraints: 12231 Sorted by residual: bond pdb=" CB TYR C 94 " pdb=" CG TYR C 94 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.20e-02 2.07e+03 3.06e+01 bond pdb=" CB TYR A 94 " pdb=" CG TYR A 94 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.20e-02 2.07e+03 3.06e+01 bond pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 1.512 1.391 0.121 2.20e-02 2.07e+03 3.05e+01 bond pdb=" CB LEU a 415 " pdb=" CG LEU a 415 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CB LEU b 415 " pdb=" CG LEU b 415 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 12226 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.53: 473 106.53 - 113.41: 6593 113.41 - 120.29: 4856 120.29 - 127.17: 4597 127.17 - 134.06: 131 Bond angle restraints: 16650 Sorted by residual: angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 112.90 121.94 -9.04 9.60e-01 1.09e+00 8.86e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 112.90 121.92 -9.02 9.60e-01 1.09e+00 8.84e+01 angle pdb=" N VAL C 65 " pdb=" CA VAL C 65 " pdb=" C VAL C 65 " ideal model delta sigma weight residual 112.90 121.92 -9.02 9.60e-01 1.09e+00 8.83e+01 angle pdb=" N PHE M 104 " pdb=" CA PHE M 104 " pdb=" C PHE M 104 " ideal model delta sigma weight residual 112.92 124.32 -11.40 1.23e+00 6.61e-01 8.59e+01 angle pdb=" N PHE J 104 " pdb=" CA PHE J 104 " pdb=" C PHE J 104 " ideal model delta sigma weight residual 112.92 124.31 -11.39 1.23e+00 6.61e-01 8.58e+01 ... (remaining 16645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 7881 21.23 - 42.46: 240 42.46 - 63.69: 36 63.69 - 84.92: 87 84.92 - 106.16: 75 Dihedral angle restraints: 8319 sinusoidal: 3639 harmonic: 4680 Sorted by residual: dihedral pdb=" CB CYS a 301 " pdb=" SG CYS a 301 " pdb=" SG CYS a 310 " pdb=" CB CYS a 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.62 85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS c 301 " pdb=" SG CYS c 301 " pdb=" SG CYS c 310 " pdb=" CB CYS c 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.62 85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS b 301 " pdb=" SG CYS b 301 " pdb=" SG CYS b 310 " pdb=" CB CYS b 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.60 85.60 1 1.00e+01 1.00e-02 8.86e+01 ... (remaining 8316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1390 0.105 - 0.209: 495 0.209 - 0.314: 186 0.314 - 0.418: 71 0.418 - 0.523: 60 Chirality restraints: 2202 Sorted by residual: chirality pdb=" C1 BMA e 3 " pdb=" O4 NAG e 2 " pdb=" C2 BMA e 3 " pdb=" O5 BMA e 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+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 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 2199 not shown) Planarity restraints: 2103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.82e+02 pdb=" C7 NAG W 1 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.82e+02 pdb=" C7 NAG i 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.81e+02 pdb=" C7 NAG I 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 2100 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4235 2.86 - 3.37: 11353 3.37 - 3.88: 19394 3.88 - 4.39: 22062 4.39 - 4.90: 34281 Nonbonded interactions: 91325 Sorted by model distance: nonbonded pdb=" O3 NAG S 2 " pdb=" O7 NAG S 2 " model vdw 2.354 2.440 nonbonded pdb=" O3 NAG D 2 " pdb=" O7 NAG D 2 " model vdw 2.355 2.440 nonbonded pdb=" O3 NAG e 2 " pdb=" O7 NAG e 2 " model vdw 2.355 2.440 nonbonded pdb=" N TYR C 200 " pdb=" N ILE C 201 " model vdw 2.381 2.560 nonbonded pdb=" N TYR B 200 " pdb=" N ILE B 201 " model vdw 2.382 2.560 ... (remaining 91320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'U' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'Y' selection = chain 'k' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 10.510 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.340 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.149 12231 Z= 1.451 Angle : 2.044 11.923 16650 Z= 1.323 Chirality : 0.151 0.523 2202 Planarity : 0.014 0.250 2070 Dihedral : 17.976 106.156 5244 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1605 helix: 0.11 (0.24), residues: 315 sheet: 0.86 (0.27), residues: 333 loop : -0.33 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP a 370 HIS 0.008 0.002 HIS a 354 PHE 0.031 0.006 PHE b 309 TYR 0.079 0.010 TYR b 363 ARG 0.002 0.001 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.6735 (mttt) cc_final: 0.6479 (mmtt) REVERT: A 144 ILE cc_start: 0.8021 (mt) cc_final: 0.7700 (mt) REVERT: A 200 TYR cc_start: 0.8807 (p90) cc_final: 0.8545 (p90) REVERT: A 217 TYR cc_start: 0.7930 (m-80) cc_final: 0.6916 (m-80) REVERT: A 227 TRP cc_start: 0.7889 (p90) cc_final: 0.7245 (p-90) REVERT: A 228 GLU cc_start: 0.8290 (pm20) cc_final: 0.7973 (pp20) REVERT: A 236 PRO cc_start: 0.8505 (Cg_endo) cc_final: 0.7930 (Cg_exo) REVERT: a 308 GLU cc_start: 0.8539 (mp0) cc_final: 0.8275 (mm-30) REVERT: a 371 TYR cc_start: 0.7382 (m-80) cc_final: 0.7112 (m-80) REVERT: a 396 GLU cc_start: 0.8773 (mp0) cc_final: 0.8567 (mp0) REVERT: B 144 ILE cc_start: 0.8029 (mt) cc_final: 0.7744 (mt) REVERT: B 217 TYR cc_start: 0.7811 (m-80) cc_final: 0.6836 (m-80) REVERT: B 227 TRP cc_start: 0.7911 (p90) cc_final: 0.7378 (p-90) REVERT: B 228 GLU cc_start: 0.8067 (pm20) cc_final: 0.7751 (pp20) REVERT: B 236 PRO cc_start: 0.8579 (Cg_endo) cc_final: 0.8051 (Cg_exo) REVERT: b 311 ASP cc_start: 0.8674 (m-30) cc_final: 0.8204 (t0) REVERT: b 371 TYR cc_start: 0.7389 (m-80) cc_final: 0.7024 (m-80) REVERT: b 396 GLU cc_start: 0.8700 (mp0) cc_final: 0.8468 (mp0) REVERT: C 78 LEU cc_start: 0.8753 (mt) cc_final: 0.8470 (mp) REVERT: C 144 ILE cc_start: 0.8057 (mt) cc_final: 0.7749 (mt) REVERT: C 211 ASP cc_start: 0.8000 (p0) cc_final: 0.7613 (p0) REVERT: C 217 TYR cc_start: 0.7983 (m-80) cc_final: 0.7076 (m-80) REVERT: C 236 PRO cc_start: 0.8575 (Cg_endo) cc_final: 0.7970 (Cg_exo) REVERT: c 311 ASP cc_start: 0.8598 (m-30) cc_final: 0.8211 (t0) REVERT: c 316 PHE cc_start: 0.8584 (m-80) cc_final: 0.8191 (m-10) REVERT: c 321 GLN cc_start: 0.8332 (mt0) cc_final: 0.7953 (mm-40) REVERT: c 396 GLU cc_start: 0.8699 (mp0) cc_final: 0.8497 (mp0) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2714 time to fit residues: 133.1192 Evaluate side-chains 188 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 141 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 321 GLN a 331 GLN a 348 GLN ** a 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 141 HIS ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN b 338 ASN b 348 GLN b 405 GLN C 92 HIS C 141 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 12231 Z= 0.413 Angle : 1.017 10.050 16650 Z= 0.513 Chirality : 0.056 0.366 2202 Planarity : 0.005 0.041 2070 Dihedral : 15.462 104.605 3450 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.58 % Allowed : 6.55 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.26 (0.19), residues: 1605 helix: 0.43 (0.27), residues: 345 sheet: 0.50 (0.29), residues: 300 loop : -0.59 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 227 HIS 0.011 0.002 HIS B 230 PHE 0.024 0.003 PHE A 233 TYR 0.027 0.004 TYR c 366 ARG 0.005 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 236 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7655 (mtm) cc_final: 0.7324 (ppp) REVERT: A 156 ASP cc_start: 0.7358 (t0) cc_final: 0.6896 (t0) REVERT: A 200 TYR cc_start: 0.8551 (p90) cc_final: 0.8280 (p90) REVERT: A 217 TYR cc_start: 0.7549 (m-80) cc_final: 0.7280 (m-80) REVERT: A 228 GLU cc_start: 0.8650 (pm20) cc_final: 0.7595 (pp20) REVERT: a 363 TYR cc_start: 0.7704 (p90) cc_final: 0.7339 (p90) REVERT: a 371 TYR cc_start: 0.6801 (m-80) cc_final: 0.6488 (m-80) REVERT: a 396 GLU cc_start: 0.8632 (mp0) cc_final: 0.8281 (mp0) REVERT: a 408 ASP cc_start: 0.7735 (t0) cc_final: 0.7442 (t70) REVERT: a 410 MET cc_start: 0.9013 (mtt) cc_final: 0.8711 (mtp) REVERT: B 96 MET cc_start: 0.7699 (mtm) cc_final: 0.7470 (ppp) REVERT: B 156 ASP cc_start: 0.7148 (t0) cc_final: 0.6770 (t0) REVERT: B 200 TYR cc_start: 0.8575 (p90) cc_final: 0.8370 (p90) REVERT: B 217 TYR cc_start: 0.7593 (m-80) cc_final: 0.7338 (m-80) REVERT: B 228 GLU cc_start: 0.8593 (pm20) cc_final: 0.7888 (pp20) REVERT: B 236 PRO cc_start: 0.9193 (Cg_endo) cc_final: 0.8928 (Cg_exo) REVERT: b 396 GLU cc_start: 0.8668 (mp0) cc_final: 0.8255 (mp0) REVERT: b 408 ASP cc_start: 0.7628 (t0) cc_final: 0.7321 (t70) REVERT: b 410 MET cc_start: 0.9204 (mtt) cc_final: 0.8933 (mtp) REVERT: C 116 LYS cc_start: 0.8132 (mttt) cc_final: 0.7541 (tptt) REVERT: C 134 MET cc_start: 0.7227 (ttp) cc_final: 0.5533 (mtt) REVERT: C 156 ASP cc_start: 0.7096 (t0) cc_final: 0.6727 (t0) REVERT: C 236 PRO cc_start: 0.9061 (Cg_endo) cc_final: 0.8833 (Cg_exo) REVERT: c 321 GLN cc_start: 0.8485 (mt0) cc_final: 0.8028 (mm-40) REVERT: c 396 GLU cc_start: 0.8699 (mp0) cc_final: 0.8448 (mp0) REVERT: c 408 ASP cc_start: 0.7854 (t0) cc_final: 0.7639 (t70) REVERT: c 410 MET cc_start: 0.8980 (mtt) cc_final: 0.8735 (mtp) outliers start: 5 outliers final: 2 residues processed: 239 average time/residue: 0.2360 time to fit residues: 80.3359 Evaluate side-chains 179 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 39 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 331 GLN a 338 ASN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 230 HIS b 331 GLN b 338 ASN ** b 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 12231 Z= 0.429 Angle : 1.006 15.171 16650 Z= 0.502 Chirality : 0.052 0.365 2202 Planarity : 0.005 0.068 2070 Dihedral : 12.825 95.212 3450 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.94 % Allowed : 7.60 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1605 helix: 0.44 (0.29), residues: 321 sheet: 0.14 (0.29), residues: 321 loop : -1.06 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP a 386 HIS 0.012 0.003 HIS c 354 PHE 0.029 0.003 PHE c 399 TYR 0.029 0.004 TYR b 371 ARG 0.007 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 212 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8664 (p90) cc_final: 0.8345 (p90) REVERT: A 217 TYR cc_start: 0.7966 (m-80) cc_final: 0.7673 (m-80) REVERT: a 311 ASP cc_start: 0.9212 (m-30) cc_final: 0.9003 (m-30) REVERT: a 351 MET cc_start: 0.9034 (mmp) cc_final: 0.8700 (tpp) REVERT: a 371 TYR cc_start: 0.7011 (m-80) cc_final: 0.6676 (m-80) REVERT: a 408 ASP cc_start: 0.7580 (t0) cc_final: 0.7267 (t70) REVERT: a 410 MET cc_start: 0.9000 (mtt) cc_final: 0.8755 (mtp) REVERT: B 217 TYR cc_start: 0.7931 (m-80) cc_final: 0.7681 (m-80) REVERT: b 308 GLU cc_start: 0.8500 (pm20) cc_final: 0.8017 (pm20) REVERT: b 311 ASP cc_start: 0.9016 (m-30) cc_final: 0.8796 (m-30) REVERT: b 371 TYR cc_start: 0.7742 (m-80) cc_final: 0.7270 (m-80) REVERT: b 408 ASP cc_start: 0.7544 (t0) cc_final: 0.7304 (t70) REVERT: b 410 MET cc_start: 0.9110 (mtt) cc_final: 0.8778 (mtp) REVERT: C 96 MET cc_start: 0.7937 (ptm) cc_final: 0.7733 (ppp) REVERT: C 116 LYS cc_start: 0.8214 (mttt) cc_final: 0.7566 (tptt) REVERT: C 125 LYS cc_start: 0.5747 (mmtt) cc_final: 0.5356 (mmtt) REVERT: C 193 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8314 (mtm-85) REVERT: C 217 TYR cc_start: 0.7616 (m-80) cc_final: 0.7321 (m-80) REVERT: c 311 ASP cc_start: 0.9150 (m-30) cc_final: 0.8801 (m-30) REVERT: c 321 GLN cc_start: 0.8498 (mt0) cc_final: 0.8136 (mm-40) REVERT: c 371 TYR cc_start: 0.7278 (m-80) cc_final: 0.7052 (m-80) REVERT: c 408 ASP cc_start: 0.7772 (t0) cc_final: 0.7561 (t70) REVERT: c 410 MET cc_start: 0.8890 (mtt) cc_final: 0.8682 (mtp) outliers start: 8 outliers final: 0 residues processed: 213 average time/residue: 0.2431 time to fit residues: 73.8224 Evaluate side-chains 174 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 153 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 331 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 406 GLN ** b 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12231 Z= 0.362 Angle : 0.897 7.770 16650 Z= 0.446 Chirality : 0.049 0.346 2202 Planarity : 0.005 0.059 2070 Dihedral : 11.584 86.375 3450 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1605 helix: 0.35 (0.28), residues: 324 sheet: 0.09 (0.28), residues: 342 loop : -1.31 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP c 386 HIS 0.009 0.002 HIS B 141 PHE 0.018 0.002 PHE C 191 TYR 0.027 0.003 TYR B 66 ARG 0.006 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7649 (ppp) cc_final: 0.6900 (ppp) REVERT: A 217 TYR cc_start: 0.7906 (m-80) cc_final: 0.7488 (m-80) REVERT: B 96 MET cc_start: 0.7703 (ppp) cc_final: 0.6972 (ppp) REVERT: B 200 TYR cc_start: 0.8689 (p90) cc_final: 0.8347 (p90) REVERT: B 217 TYR cc_start: 0.8009 (m-80) cc_final: 0.7635 (m-80) REVERT: b 311 ASP cc_start: 0.9035 (m-30) cc_final: 0.8804 (m-30) REVERT: b 333 SER cc_start: 0.9242 (p) cc_final: 0.8963 (m) REVERT: b 371 TYR cc_start: 0.7658 (m-80) cc_final: 0.7319 (m-80) REVERT: C 84 LEU cc_start: 0.7320 (mp) cc_final: 0.7073 (mp) REVERT: C 96 MET cc_start: 0.7610 (ptt) cc_final: 0.7325 (ppp) REVERT: C 116 LYS cc_start: 0.8198 (mttt) cc_final: 0.7563 (tptt) REVERT: C 125 LYS cc_start: 0.5822 (mmtt) cc_final: 0.5549 (mmtt) REVERT: C 134 MET cc_start: 0.7661 (tmm) cc_final: 0.7142 (ttt) REVERT: C 193 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8337 (mtm-85) REVERT: c 284 MET cc_start: 0.8111 (ptp) cc_final: 0.7693 (ptp) REVERT: c 311 ASP cc_start: 0.9020 (m-30) cc_final: 0.8553 (m-30) REVERT: c 321 GLN cc_start: 0.8448 (mt0) cc_final: 0.8111 (mm-40) REVERT: c 371 TYR cc_start: 0.7401 (m-80) cc_final: 0.7020 (m-80) REVERT: c 410 MET cc_start: 0.8993 (mtt) cc_final: 0.8769 (mtp) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.2314 time to fit residues: 73.9902 Evaluate side-chains 171 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 30.0000 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 338 ASN a 374 HIS ** a 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 HIS ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12231 Z= 0.352 Angle : 0.878 9.333 16650 Z= 0.437 Chirality : 0.048 0.343 2202 Planarity : 0.005 0.052 2070 Dihedral : 11.031 78.250 3450 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.39 % 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: -1.37 (0.20), residues: 1605 helix: -0.07 (0.28), residues: 324 sheet: -0.09 (0.28), residues: 342 loop : -1.58 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 210 HIS 0.008 0.002 HIS A 141 PHE 0.026 0.003 PHE C 157 TYR 0.021 0.003 TYR a 366 ARG 0.006 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7846 (ppp) cc_final: 0.7185 (ppp) REVERT: A 200 TYR cc_start: 0.8457 (p90) cc_final: 0.8208 (p90) REVERT: A 217 TYR cc_start: 0.7982 (m-80) cc_final: 0.7513 (m-80) REVERT: a 311 ASP cc_start: 0.9167 (m-30) cc_final: 0.8650 (m-30) REVERT: B 80 MET cc_start: 0.8841 (mtt) cc_final: 0.8506 (mtt) REVERT: B 96 MET cc_start: 0.7856 (ppp) cc_final: 0.7208 (ppp) REVERT: B 200 TYR cc_start: 0.8712 (p90) cc_final: 0.8407 (p90) REVERT: B 217 TYR cc_start: 0.8031 (m-80) cc_final: 0.7589 (m-80) REVERT: b 284 MET cc_start: 0.8439 (ptp) cc_final: 0.8097 (ptp) REVERT: b 311 ASP cc_start: 0.9097 (m-30) cc_final: 0.8763 (m-30) REVERT: b 333 SER cc_start: 0.9168 (p) cc_final: 0.8753 (m) REVERT: b 334 ILE cc_start: 0.8939 (mm) cc_final: 0.8646 (mm) REVERT: b 371 TYR cc_start: 0.7642 (m-80) cc_final: 0.7250 (m-80) REVERT: C 116 LYS cc_start: 0.8203 (mttt) cc_final: 0.7509 (tptt) REVERT: C 134 MET cc_start: 0.7750 (tmm) cc_final: 0.7265 (ttt) REVERT: C 214 MET cc_start: 0.8346 (tpp) cc_final: 0.7916 (tpt) REVERT: c 311 ASP cc_start: 0.9013 (m-30) cc_final: 0.8517 (m-30) REVERT: c 321 GLN cc_start: 0.8487 (mt0) cc_final: 0.8092 (mm-40) REVERT: c 371 TYR cc_start: 0.7346 (m-80) cc_final: 0.6965 (m-80) REVERT: c 410 MET cc_start: 0.8849 (mtt) cc_final: 0.8459 (mtp) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.2303 time to fit residues: 71.7011 Evaluate side-chains 176 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 40.0000 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 153 optimal weight: 0.0010 chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12231 Z= 0.232 Angle : 0.801 8.799 16650 Z= 0.395 Chirality : 0.048 0.346 2202 Planarity : 0.004 0.052 2070 Dihedral : 10.458 69.240 3450 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.12 % Allowed : 2.81 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1605 helix: 0.29 (0.29), residues: 327 sheet: -0.34 (0.29), residues: 324 loop : -1.35 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 210 HIS 0.004 0.001 HIS B 124 PHE 0.023 0.002 PHE C 191 TYR 0.023 0.002 TYR A 66 ARG 0.007 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7912 (ppp) cc_final: 0.7295 (ppp) REVERT: A 228 GLU cc_start: 0.8261 (pm20) cc_final: 0.7812 (pp20) REVERT: A 229 ASP cc_start: 0.7509 (t0) cc_final: 0.7162 (t0) REVERT: a 284 MET cc_start: 0.7779 (pmm) cc_final: 0.7484 (pmm) REVERT: a 311 ASP cc_start: 0.9059 (m-30) cc_final: 0.8612 (m-30) REVERT: a 351 MET cc_start: 0.9012 (mmp) cc_final: 0.8695 (tpp) REVERT: a 410 MET cc_start: 0.8740 (mtt) cc_final: 0.8333 (mtt) REVERT: B 82 MET cc_start: 0.8793 (ptp) cc_final: 0.8428 (pmm) REVERT: B 96 MET cc_start: 0.7904 (ppp) cc_final: 0.7186 (ppp) REVERT: B 193 ARG cc_start: 0.8636 (mtm-85) cc_final: 0.8393 (mtm-85) REVERT: B 200 TYR cc_start: 0.8568 (p90) cc_final: 0.8337 (p90) REVERT: B 217 TYR cc_start: 0.7865 (m-80) cc_final: 0.7365 (m-80) REVERT: b 284 MET cc_start: 0.8350 (ptp) cc_final: 0.7876 (ptp) REVERT: b 311 ASP cc_start: 0.8999 (m-30) cc_final: 0.8568 (m-30) REVERT: b 410 MET cc_start: 0.8877 (mtt) cc_final: 0.8535 (mtt) REVERT: C 80 MET cc_start: 0.8883 (mtm) cc_final: 0.8546 (mmt) REVERT: C 82 MET cc_start: 0.9118 (ptp) cc_final: 0.8462 (pmm) REVERT: C 96 MET cc_start: 0.8168 (ppp) cc_final: 0.7518 (ppp) REVERT: C 116 LYS cc_start: 0.8173 (mttt) cc_final: 0.7481 (tptt) REVERT: C 191 PHE cc_start: 0.8387 (t80) cc_final: 0.8154 (t80) REVERT: C 193 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8407 (mmm-85) REVERT: C 214 MET cc_start: 0.8272 (tpp) cc_final: 0.7784 (tpt) REVERT: c 284 MET cc_start: 0.8490 (ptp) cc_final: 0.8216 (ptp) REVERT: c 311 ASP cc_start: 0.8928 (m-30) cc_final: 0.8428 (m-30) REVERT: c 321 GLN cc_start: 0.8425 (mt0) cc_final: 0.8059 (mm-40) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.2381 time to fit residues: 77.7960 Evaluate side-chains 181 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.3980 chunk 87 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 85 optimal weight: 40.0000 chunk 153 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12231 Z= 0.293 Angle : 0.820 9.006 16650 Z= 0.406 Chirality : 0.048 0.336 2202 Planarity : 0.004 0.051 2070 Dihedral : 10.225 66.029 3450 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -1.37 (0.20), residues: 1605 helix: 0.10 (0.28), residues: 327 sheet: -0.40 (0.28), residues: 327 loop : -1.50 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 210 HIS 0.006 0.002 HIS A 124 PHE 0.019 0.002 PHE B 191 TYR 0.020 0.002 TYR c 371 ARG 0.008 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7961 (ppp) cc_final: 0.7302 (ppp) REVERT: a 284 MET cc_start: 0.7738 (pmm) cc_final: 0.7381 (pmm) REVERT: a 311 ASP cc_start: 0.9120 (m-30) cc_final: 0.8581 (m-30) REVERT: a 323 ILE cc_start: 0.8973 (tp) cc_final: 0.8458 (tp) REVERT: a 351 MET cc_start: 0.8976 (mmp) cc_final: 0.8697 (tpp) REVERT: a 410 MET cc_start: 0.8850 (mtt) cc_final: 0.8456 (mtt) REVERT: B 75 MET cc_start: 0.7900 (mtt) cc_final: 0.7585 (mtt) REVERT: B 96 MET cc_start: 0.7881 (ppp) cc_final: 0.7186 (ppp) REVERT: B 193 ARG cc_start: 0.8769 (mtm-85) cc_final: 0.8443 (mtm-85) REVERT: B 200 TYR cc_start: 0.8571 (p90) cc_final: 0.8324 (p90) REVERT: B 217 TYR cc_start: 0.8036 (m-80) cc_final: 0.7475 (m-80) REVERT: b 284 MET cc_start: 0.8059 (ptp) cc_final: 0.7731 (ptp) REVERT: b 311 ASP cc_start: 0.8979 (m-30) cc_final: 0.8394 (m-30) REVERT: b 410 MET cc_start: 0.8860 (mtt) cc_final: 0.8643 (mtp) REVERT: C 80 MET cc_start: 0.8900 (mtm) cc_final: 0.8588 (mmt) REVERT: C 96 MET cc_start: 0.8056 (ppp) cc_final: 0.7395 (ppp) REVERT: C 116 LYS cc_start: 0.8103 (mttt) cc_final: 0.7425 (tptt) REVERT: C 191 PHE cc_start: 0.8485 (t80) cc_final: 0.8279 (t80) REVERT: C 193 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8537 (mmm-85) REVERT: C 214 MET cc_start: 0.8331 (tpp) cc_final: 0.7845 (tpt) REVERT: c 284 MET cc_start: 0.8260 (ptp) cc_final: 0.7912 (ptp) REVERT: c 311 ASP cc_start: 0.8942 (m-30) cc_final: 0.8420 (m-30) REVERT: c 321 GLN cc_start: 0.8457 (mt0) cc_final: 0.8070 (mm-40) REVERT: c 333 SER cc_start: 0.9305 (p) cc_final: 0.9098 (p) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2439 time to fit residues: 74.1802 Evaluate side-chains 169 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 146 optimal weight: 40.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12231 Z= 0.311 Angle : 0.851 8.656 16650 Z= 0.423 Chirality : 0.048 0.331 2202 Planarity : 0.004 0.051 2070 Dihedral : 10.053 61.152 3450 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1605 helix: -0.11 (0.28), residues: 327 sheet: -0.56 (0.26), residues: 342 loop : -1.60 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 210 HIS 0.008 0.002 HIS C 230 PHE 0.019 0.002 PHE B 157 TYR 0.022 0.002 TYR a 363 ARG 0.004 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8092 (ppp) cc_final: 0.7482 (ppp) REVERT: a 284 MET cc_start: 0.7780 (pmm) cc_final: 0.7346 (pmm) REVERT: a 311 ASP cc_start: 0.9087 (m-30) cc_final: 0.8571 (m-30) REVERT: a 345 ILE cc_start: 0.8604 (pt) cc_final: 0.8388 (pt) REVERT: a 351 MET cc_start: 0.8877 (mmp) cc_final: 0.8604 (tpp) REVERT: a 410 MET cc_start: 0.8771 (mtt) cc_final: 0.8394 (mtt) REVERT: B 75 MET cc_start: 0.7792 (mtt) cc_final: 0.7520 (tpp) REVERT: B 96 MET cc_start: 0.8064 (ppp) cc_final: 0.7337 (ppp) REVERT: B 193 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8324 (mtm-85) REVERT: B 200 TYR cc_start: 0.8583 (p90) cc_final: 0.8375 (p90) REVERT: B 217 TYR cc_start: 0.8039 (m-80) cc_final: 0.7443 (m-80) REVERT: b 284 MET cc_start: 0.8034 (ptp) cc_final: 0.7636 (ptp) REVERT: b 308 GLU cc_start: 0.8143 (pm20) cc_final: 0.7666 (mp0) REVERT: b 311 ASP cc_start: 0.8912 (m-30) cc_final: 0.8297 (m-30) REVERT: b 410 MET cc_start: 0.8844 (mtt) cc_final: 0.8622 (mtp) REVERT: C 80 MET cc_start: 0.8898 (mtm) cc_final: 0.8560 (mmt) REVERT: C 82 MET cc_start: 0.9126 (ptp) cc_final: 0.8465 (pmm) REVERT: C 96 MET cc_start: 0.8127 (ppp) cc_final: 0.7482 (ppp) REVERT: C 116 LYS cc_start: 0.8092 (mttt) cc_final: 0.7399 (tptt) REVERT: C 193 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.8577 (mmm-85) REVERT: C 214 MET cc_start: 0.8369 (tpp) cc_final: 0.8001 (tpp) REVERT: c 284 MET cc_start: 0.8252 (ptp) cc_final: 0.7823 (ptp) REVERT: c 311 ASP cc_start: 0.8926 (m-30) cc_final: 0.8428 (m-30) REVERT: c 321 GLN cc_start: 0.8452 (mt0) cc_final: 0.8028 (mm-40) REVERT: c 334 ILE cc_start: 0.8108 (mp) cc_final: 0.7899 (mm) REVERT: c 411 ILE cc_start: 0.8505 (mm) cc_final: 0.8283 (mm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2365 time to fit residues: 69.3496 Evaluate side-chains 167 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 85 optimal weight: 40.0000 chunk 62 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 0.0370 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 151 optimal weight: 9.9990 overall best weight: 5.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 338 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 12231 Z= 0.451 Angle : 0.993 9.137 16650 Z= 0.497 Chirality : 0.053 0.406 2202 Planarity : 0.005 0.051 2070 Dihedral : 10.698 61.365 3450 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1605 helix: -0.68 (0.26), residues: 324 sheet: -1.02 (0.26), residues: 336 loop : -1.97 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 210 HIS 0.012 0.002 HIS C 230 PHE 0.030 0.003 PHE B 157 TYR 0.024 0.003 TYR A 94 ARG 0.004 0.001 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8005 (p90) cc_final: 0.7753 (p90) REVERT: A 96 MET cc_start: 0.8184 (ppp) cc_final: 0.7561 (ppp) REVERT: a 284 MET cc_start: 0.7834 (pmm) cc_final: 0.7409 (pmm) REVERT: a 311 ASP cc_start: 0.9168 (m-30) cc_final: 0.8604 (m-30) REVERT: a 336 LEU cc_start: 0.9284 (tp) cc_final: 0.9066 (tp) REVERT: a 351 MET cc_start: 0.9096 (mmp) cc_final: 0.8791 (tpp) REVERT: a 410 MET cc_start: 0.8914 (mtt) cc_final: 0.8713 (mtp) REVERT: B 75 MET cc_start: 0.7846 (mtt) cc_final: 0.7501 (tpp) REVERT: B 80 MET cc_start: 0.8575 (mtt) cc_final: 0.8013 (mmt) REVERT: B 96 MET cc_start: 0.8048 (ppp) cc_final: 0.7388 (ppp) REVERT: B 217 TYR cc_start: 0.8174 (m-80) cc_final: 0.7569 (m-80) REVERT: b 284 MET cc_start: 0.7985 (ptp) cc_final: 0.7596 (ptp) REVERT: b 311 ASP cc_start: 0.8940 (m-30) cc_final: 0.8307 (m-30) REVERT: b 410 MET cc_start: 0.9077 (mtt) cc_final: 0.8780 (mtp) REVERT: C 80 MET cc_start: 0.8945 (mtm) cc_final: 0.8416 (mmm) REVERT: C 82 MET cc_start: 0.9202 (ptp) cc_final: 0.8562 (pmm) REVERT: C 94 TYR cc_start: 0.8143 (p90) cc_final: 0.7922 (p90) REVERT: C 96 MET cc_start: 0.8257 (ppp) cc_final: 0.7491 (ppp) REVERT: C 116 LYS cc_start: 0.8161 (mttt) cc_final: 0.7478 (tptt) REVERT: C 134 MET cc_start: 0.7512 (tmm) cc_final: 0.7079 (ttt) REVERT: C 161 LYS cc_start: 0.8530 (pttm) cc_final: 0.8327 (pttp) REVERT: C 193 ARG cc_start: 0.8833 (mtm-85) cc_final: 0.8605 (mmm-85) REVERT: C 214 MET cc_start: 0.8275 (tpp) cc_final: 0.7848 (tpt) REVERT: c 311 ASP cc_start: 0.8944 (m-30) cc_final: 0.8422 (m-30) REVERT: c 321 GLN cc_start: 0.8422 (mt0) cc_final: 0.7807 (mm-40) REVERT: c 325 ARG cc_start: 0.8889 (mpt180) cc_final: 0.7870 (mpt180) REVERT: c 332 MET cc_start: 0.7146 (mtt) cc_final: 0.6940 (mtt) REVERT: c 345 ILE cc_start: 0.8653 (pt) cc_final: 0.8451 (pt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2374 time to fit residues: 66.1345 Evaluate side-chains 156 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 50.0000 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 40.0000 chunk 134 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12231 Z= 0.228 Angle : 0.821 9.298 16650 Z= 0.405 Chirality : 0.050 0.336 2202 Planarity : 0.004 0.051 2070 Dihedral : 9.809 58.026 3450 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.20), residues: 1605 helix: -0.03 (0.29), residues: 324 sheet: -0.95 (0.26), residues: 333 loop : -1.60 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 210 HIS 0.006 0.001 HIS C 141 PHE 0.014 0.002 PHE C 191 TYR 0.019 0.002 TYR a 363 ARG 0.005 0.001 ARG a 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8018 (ppp) cc_final: 0.7452 (ppp) REVERT: A 161 LYS cc_start: 0.8335 (pttt) cc_final: 0.8037 (pttp) REVERT: A 228 GLU cc_start: 0.8377 (pm20) cc_final: 0.7746 (pp20) REVERT: A 229 ASP cc_start: 0.7765 (t0) cc_final: 0.7312 (t0) REVERT: a 284 MET cc_start: 0.7831 (pmm) cc_final: 0.7270 (pmm) REVERT: a 311 ASP cc_start: 0.9132 (m-30) cc_final: 0.8644 (m-30) REVERT: a 351 MET cc_start: 0.8833 (mmp) cc_final: 0.8591 (tpp) REVERT: a 410 MET cc_start: 0.8772 (mtt) cc_final: 0.8478 (mtp) REVERT: B 96 MET cc_start: 0.7861 (ppp) cc_final: 0.7207 (ppp) REVERT: B 189 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8484 (tp40) REVERT: b 284 MET cc_start: 0.7897 (ptp) cc_final: 0.7528 (ptp) REVERT: b 311 ASP cc_start: 0.8928 (m-30) cc_final: 0.8329 (m-30) REVERT: b 410 MET cc_start: 0.8879 (mtt) cc_final: 0.8631 (mtp) REVERT: C 80 MET cc_start: 0.8875 (mtm) cc_final: 0.8423 (mmt) REVERT: C 82 MET cc_start: 0.8999 (ptp) cc_final: 0.8398 (pmm) REVERT: C 94 TYR cc_start: 0.8145 (p90) cc_final: 0.7935 (p90) REVERT: C 96 MET cc_start: 0.8187 (ppp) cc_final: 0.7602 (ppp) REVERT: C 116 LYS cc_start: 0.8063 (mttt) cc_final: 0.7362 (tptt) REVERT: C 134 MET cc_start: 0.7523 (tmm) cc_final: 0.7087 (ttt) REVERT: C 193 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8562 (mmm-85) REVERT: c 311 ASP cc_start: 0.8889 (m-30) cc_final: 0.8499 (m-30) REVERT: c 321 GLN cc_start: 0.8406 (mt0) cc_final: 0.7914 (mm-40) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2366 time to fit residues: 69.8142 Evaluate side-chains 166 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 40.0000 chunk 126 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.072371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.060796 restraints weight = 78196.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.062121 restraints weight = 51207.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.063036 restraints weight = 37951.140| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.7259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12231 Z= 0.293 Angle : 0.843 8.451 16650 Z= 0.417 Chirality : 0.048 0.329 2202 Planarity : 0.004 0.050 2070 Dihedral : 9.707 56.991 3450 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1605 helix: -0.24 (0.28), residues: 327 sheet: -0.97 (0.26), residues: 333 loop : -1.66 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 210 HIS 0.007 0.002 HIS C 230 PHE 0.040 0.002 PHE A 233 TYR 0.039 0.002 TYR a 371 ARG 0.009 0.001 ARG B 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.23 seconds wall clock time: 43 minutes 48.61 seconds (2628.61 seconds total)