Starting phenix.real_space_refine on Fri Jan 19 17:32:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/01_2024/7sgf_25109.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/01_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_25109/01_2024/7sgf_25109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/01_2024/7sgf_25109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/01_2024/7sgf_25109.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/01_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-1.21-5211/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: 9 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: 9 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: 9 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: 6.72, per 1000 atoms: 0.56 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: 6.19 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: 1.33 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: 3.82 Time building geometry restraints manager: 6.50 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: 7767 21.23 - 42.46: 240 42.46 - 63.69: 36 63.69 - 84.92: 87 84.92 - 106.16: 75 Dihedral angle restraints: 8205 sinusoidal: 3525 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 8202 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.500 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.450 Find NCS groups from input model: 0.810 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.200 ------------------------------------------------------------------------------- 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 : 18.157 106.156 5130 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 : 1.286 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: 0.2753 time to fit residues: 135.2389 Evaluate side-chains 188 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 218 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: 0.7263 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 12231 Z= 0.406 Angle : 1.007 9.526 16650 Z= 0.508 Chirality : 0.055 0.359 2202 Planarity : 0.005 0.039 2070 Dihedral : 15.745 104.605 3336 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.70 % Allowed : 6.55 % Favored : 92.75 % 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: 0.41 (0.27), residues: 345 sheet: 0.67 (0.28), residues: 318 loop : -0.68 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 227 HIS 0.014 0.003 HIS B 230 PHE 0.024 0.003 PHE A 233 TYR 0.031 0.004 TYR B 66 ARG 0.005 0.001 ARG b 325 *********************** 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: 6 poor density : 235 time to evaluate : 1.408 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: 0.7668 (mtm) cc_final: 0.7376 (ppp) REVERT: A 156 ASP cc_start: 0.7359 (t0) cc_final: 0.6919 (t0) REVERT: A 200 TYR cc_start: 0.8553 (p90) cc_final: 0.8281 (p90) REVERT: A 217 TYR cc_start: 0.7520 (m-80) cc_final: 0.7236 (m-80) REVERT: A 228 GLU cc_start: 0.8654 (pm20) cc_final: 0.7643 (pp20) REVERT: a 335 GLN cc_start: 0.8974 (pm20) cc_final: 0.8612 (pm20) REVERT: a 336 LEU cc_start: 0.9150 (tp) cc_final: 0.8744 (tp) REVERT: a 339 LYS cc_start: 0.9335 (mppt) cc_final: 0.9097 (mptt) REVERT: a 363 TYR cc_start: 0.7614 (p90) cc_final: 0.7207 (p90) REVERT: a 371 TYR cc_start: 0.6762 (m-80) cc_final: 0.6452 (m-80) REVERT: a 396 GLU cc_start: 0.8636 (mp0) cc_final: 0.8344 (mp0) REVERT: a 408 ASP cc_start: 0.7720 (t0) cc_final: 0.7422 (t70) REVERT: a 410 MET cc_start: 0.8971 (mtt) cc_final: 0.8669 (mtp) REVERT: B 96 MET cc_start: 0.7719 (mtm) cc_final: 0.7479 (ppp) REVERT: B 156 ASP cc_start: 0.7179 (t0) cc_final: 0.6829 (t0) REVERT: B 200 TYR cc_start: 0.8557 (p90) cc_final: 0.8338 (p90) REVERT: B 217 TYR cc_start: 0.7593 (m-80) cc_final: 0.7203 (m-80) REVERT: B 228 GLU cc_start: 0.8604 (pm20) cc_final: 0.7891 (pp20) REVERT: B 236 PRO cc_start: 0.9191 (Cg_endo) cc_final: 0.8926 (Cg_exo) REVERT: b 335 GLN cc_start: 0.8890 (pm20) cc_final: 0.8587 (pm20) REVERT: b 396 GLU cc_start: 0.8653 (mp0) cc_final: 0.8336 (mp0) REVERT: b 408 ASP cc_start: 0.7631 (t0) cc_final: 0.7321 (t70) REVERT: b 410 MET cc_start: 0.9196 (mtt) cc_final: 0.8959 (mtp) REVERT: C 116 LYS cc_start: 0.8128 (mttt) cc_final: 0.7540 (tptt) REVERT: C 134 MET cc_start: 0.7184 (ttp) cc_final: 0.5472 (mtt) REVERT: C 156 ASP cc_start: 0.7095 (t0) cc_final: 0.6716 (t0) REVERT: C 194 MET cc_start: 0.8288 (ptp) cc_final: 0.7882 (ptp) REVERT: C 236 PRO cc_start: 0.9054 (Cg_endo) cc_final: 0.8814 (Cg_exo) REVERT: c 321 GLN cc_start: 0.8483 (mt0) cc_final: 0.8033 (mm-40) REVERT: c 396 GLU cc_start: 0.8691 (mp0) cc_final: 0.8449 (mp0) REVERT: c 408 ASP cc_start: 0.7858 (t0) cc_final: 0.7643 (t70) REVERT: c 410 MET cc_start: 0.8958 (mtt) cc_final: 0.8687 (mtp) outliers start: 6 outliers final: 2 residues processed: 239 average time/residue: 0.2417 time to fit residues: 82.3538 Evaluate side-chains 178 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 39 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 0.0970 chunk 143 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 chunk 116 optimal weight: 3.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 338 ASN a 374 HIS ** a 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS b 338 ASN b 374 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS c 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 12231 Z= 0.317 Angle : 0.858 10.468 16650 Z= 0.427 Chirality : 0.049 0.356 2202 Planarity : 0.004 0.053 2070 Dihedral : 12.994 93.162 3336 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.47 % Allowed : 5.15 % 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: -0.35 (0.20), residues: 1605 helix: 0.76 (0.29), residues: 342 sheet: 0.53 (0.28), residues: 315 loop : -0.89 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP a 386 HIS 0.006 0.001 HIS A 141 PHE 0.029 0.002 PHE b 399 TYR 0.033 0.003 TYR C 66 ARG 0.005 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 235 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.398 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 156 ASP cc_start: 0.7355 (t0) cc_final: 0.7106 (t70) REVERT: A 200 TYR cc_start: 0.8524 (p90) cc_final: 0.8227 (p90) REVERT: A 217 TYR cc_start: 0.7515 (m-80) cc_final: 0.7153 (m-80) REVERT: A 228 GLU cc_start: 0.8396 (pm20) cc_final: 0.7709 (pp20) REVERT: a 351 MET cc_start: 0.8849 (mmp) cc_final: 0.8554 (tpp) REVERT: a 371 TYR cc_start: 0.6942 (m-80) cc_final: 0.6614 (m-80) REVERT: a 408 ASP cc_start: 0.7671 (t0) cc_final: 0.7353 (t70) REVERT: a 410 MET cc_start: 0.9017 (mtt) cc_final: 0.8764 (mtp) REVERT: B 156 ASP cc_start: 0.7395 (t0) cc_final: 0.7174 (t70) REVERT: B 200 TYR cc_start: 0.8524 (p90) cc_final: 0.8276 (p90) REVERT: B 217 TYR cc_start: 0.7537 (m-80) cc_final: 0.7225 (m-80) REVERT: B 228 GLU cc_start: 0.8486 (pm20) cc_final: 0.7495 (pp20) REVERT: b 371 TYR cc_start: 0.7481 (m-80) cc_final: 0.6843 (m-80) REVERT: b 408 ASP cc_start: 0.7539 (t0) cc_final: 0.7250 (t70) REVERT: C 116 LYS cc_start: 0.8190 (mttt) cc_final: 0.7605 (tptt) REVERT: C 134 MET cc_start: 0.7106 (ttp) cc_final: 0.5679 (mtt) REVERT: C 156 ASP cc_start: 0.7161 (t0) cc_final: 0.6915 (t70) REVERT: C 217 TYR cc_start: 0.7441 (m-80) cc_final: 0.6898 (m-80) REVERT: c 371 TYR cc_start: 0.7154 (m-80) cc_final: 0.6768 (m-80) REVERT: c 408 ASP cc_start: 0.7844 (t0) cc_final: 0.7626 (t70) outliers start: 4 outliers final: 0 residues processed: 231 average time/residue: 0.2377 time to fit residues: 78.3375 Evaluate side-chains 188 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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: 8.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 230 HIS b 331 GLN b 338 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 12231 Z= 0.444 Angle : 1.011 9.411 16650 Z= 0.499 Chirality : 0.052 0.421 2202 Planarity : 0.005 0.048 2070 Dihedral : 11.512 84.782 3336 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 29.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.47 % Allowed : 7.02 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.06 (0.20), residues: 1605 helix: -0.02 (0.27), residues: 327 sheet: -0.04 (0.29), residues: 327 loop : -1.22 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 210 HIS 0.010 0.003 HIS A 124 PHE 0.030 0.003 PHE c 399 TYR 0.028 0.004 TYR c 366 ARG 0.005 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 217 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 1.348 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 75 MET cc_start: 0.7847 (mpp) cc_final: 0.7518 (mmm) REVERT: A 96 MET cc_start: 0.7404 (ppp) cc_final: 0.6737 (ppp) REVERT: A 217 TYR cc_start: 0.7957 (m-80) cc_final: 0.7586 (m-80) REVERT: a 311 ASP cc_start: 0.9199 (m-30) cc_final: 0.8892 (m-30) REVERT: a 396 GLU cc_start: 0.8753 (mp0) cc_final: 0.8476 (mp0) REVERT: a 408 ASP cc_start: 0.7675 (t0) cc_final: 0.7334 (t70) REVERT: B 96 MET cc_start: 0.7865 (ppp) cc_final: 0.7387 (ppp) REVERT: B 193 ARG cc_start: 0.8824 (mtm-85) cc_final: 0.8418 (mtm-85) REVERT: B 217 TYR cc_start: 0.8103 (m-80) cc_final: 0.7778 (m-80) REVERT: B 227 TRP cc_start: 0.7855 (p90) cc_final: 0.7465 (p-90) REVERT: b 311 ASP cc_start: 0.9027 (m-30) cc_final: 0.8763 (m-30) REVERT: b 332 MET cc_start: 0.7817 (mtp) cc_final: 0.7231 (mtt) REVERT: b 333 SER cc_start: 0.9308 (p) cc_final: 0.9030 (m) REVERT: b 371 TYR cc_start: 0.7760 (m-80) cc_final: 0.7299 (m-80) REVERT: b 408 ASP cc_start: 0.7540 (t0) cc_final: 0.7280 (t70) REVERT: b 410 MET cc_start: 0.8905 (mtt) cc_final: 0.8618 (mtp) REVERT: C 96 MET cc_start: 0.7862 (ppp) cc_final: 0.7235 (ppp) REVERT: C 116 LYS cc_start: 0.8229 (mttt) cc_final: 0.7634 (tptt) REVERT: C 134 MET cc_start: 0.7427 (ttp) cc_final: 0.5977 (mtt) REVERT: C 217 TYR cc_start: 0.7727 (m-80) cc_final: 0.7524 (m-80) REVERT: c 311 ASP cc_start: 0.9072 (m-30) cc_final: 0.8725 (m-30) REVERT: c 321 GLN cc_start: 0.8515 (mt0) cc_final: 0.8125 (mm-40) REVERT: c 332 MET cc_start: 0.7894 (mtp) cc_final: 0.6966 (mtt) REVERT: c 335 GLN cc_start: 0.9347 (pm20) cc_final: 0.8974 (pm20) REVERT: c 371 TYR cc_start: 0.7553 (m-80) cc_final: 0.7153 (m-80) REVERT: c 408 ASP cc_start: 0.7695 (t0) cc_final: 0.7456 (t70) REVERT: c 410 MET cc_start: 0.8844 (mtt) cc_final: 0.8547 (mtp) outliers start: 4 outliers final: 2 residues processed: 215 average time/residue: 0.2406 time to fit residues: 74.1666 Evaluate side-chains 180 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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: 40.0000 chunk 2 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.0470 chunk 137 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN a 331 GLN a 406 GLN B 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12231 Z= 0.252 Angle : 0.799 9.038 16650 Z= 0.395 Chirality : 0.047 0.338 2202 Planarity : 0.004 0.052 2070 Dihedral : 10.261 71.920 3336 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: -0.88 (0.20), residues: 1605 helix: 0.49 (0.29), residues: 327 sheet: 0.02 (0.29), residues: 339 loop : -1.24 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 210 HIS 0.020 0.001 HIS B 141 PHE 0.022 0.002 PHE C 191 TYR 0.021 0.002 TYR a 371 ARG 0.005 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 229 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7546 (mpp) cc_final: 0.7340 (mmm) REVERT: A 80 MET cc_start: 0.8742 (mtt) cc_final: 0.8467 (mtt) REVERT: A 96 MET cc_start: 0.7600 (ppp) cc_final: 0.6981 (ppp) REVERT: A 227 TRP cc_start: 0.7779 (p90) cc_final: 0.7564 (p90) REVERT: A 228 GLU cc_start: 0.8223 (pm20) cc_final: 0.7677 (pp20) REVERT: A 229 ASP cc_start: 0.7466 (t0) cc_final: 0.7171 (t0) REVERT: a 311 ASP cc_start: 0.9078 (m-30) cc_final: 0.8559 (m-30) REVERT: a 351 MET cc_start: 0.9012 (mmp) cc_final: 0.8566 (tpp) REVERT: a 408 ASP cc_start: 0.7677 (t0) cc_final: 0.7323 (t70) REVERT: B 96 MET cc_start: 0.7798 (ppp) cc_final: 0.7257 (ppp) REVERT: B 200 TYR cc_start: 0.8547 (p90) cc_final: 0.8275 (p90) REVERT: B 217 TYR cc_start: 0.7792 (m-80) cc_final: 0.7417 (m-80) REVERT: B 227 TRP cc_start: 0.7808 (p90) cc_final: 0.7494 (p-90) REVERT: b 311 ASP cc_start: 0.8905 (m-30) cc_final: 0.8556 (m-30) REVERT: b 333 SER cc_start: 0.9172 (p) cc_final: 0.8908 (m) REVERT: b 371 TYR cc_start: 0.7424 (m-80) cc_final: 0.7029 (m-80) REVERT: b 408 ASP cc_start: 0.7646 (t0) cc_final: 0.7349 (t70) REVERT: b 410 MET cc_start: 0.8950 (mtt) cc_final: 0.8745 (mtp) REVERT: C 75 MET cc_start: 0.8138 (mmt) cc_final: 0.7725 (mmt) REVERT: C 96 MET cc_start: 0.7677 (ppp) cc_final: 0.7113 (ppp) REVERT: C 116 LYS cc_start: 0.8171 (mttt) cc_final: 0.7484 (tptt) REVERT: C 134 MET cc_start: 0.7274 (ttp) cc_final: 0.5860 (mtt) REVERT: C 142 LEU cc_start: 0.9099 (pp) cc_final: 0.8879 (mm) REVERT: c 311 ASP cc_start: 0.8969 (m-30) cc_final: 0.8461 (m-30) REVERT: c 321 GLN cc_start: 0.8430 (mt0) cc_final: 0.8062 (mm-40) REVERT: c 335 GLN cc_start: 0.9195 (pm20) cc_final: 0.8827 (pm20) REVERT: c 371 TYR cc_start: 0.7374 (m-80) cc_final: 0.7068 (m-80) REVERT: c 408 ASP cc_start: 0.7661 (t0) cc_final: 0.7417 (t70) REVERT: c 410 MET cc_start: 0.8904 (mtt) cc_final: 0.8641 (mtp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2399 time to fit residues: 78.1150 Evaluate side-chains 177 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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: 9.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 80 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 overall best weight: 4.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 331 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12231 Z= 0.357 Angle : 0.892 10.847 16650 Z= 0.440 Chirality : 0.050 0.340 2202 Planarity : 0.005 0.058 2070 Dihedral : 10.165 66.577 3336 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.12 % Allowed : 5.85 % Favored : 94.04 % 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: -1.34 (0.20), residues: 1605 helix: 0.17 (0.28), residues: 327 sheet: -0.24 (0.27), residues: 342 loop : -1.58 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 227 HIS 0.011 0.002 HIS C 230 PHE 0.019 0.002 PHE C 191 TYR 0.019 0.003 TYR c 393 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 218 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.299 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: 0.7876 (ppp) cc_final: 0.7192 (ppp) REVERT: A 200 TYR cc_start: 0.8445 (p90) cc_final: 0.8229 (p90) REVERT: a 311 ASP cc_start: 0.9100 (m-30) cc_final: 0.8522 (m-30) REVERT: a 351 MET cc_start: 0.8991 (mmp) cc_final: 0.8615 (tpp) REVERT: B 96 MET cc_start: 0.7958 (ppp) cc_final: 0.7238 (ppp) REVERT: B 200 TYR cc_start: 0.8792 (p90) cc_final: 0.8487 (p90) REVERT: B 217 TYR cc_start: 0.7942 (m-80) cc_final: 0.7523 (m-80) REVERT: B 227 TRP cc_start: 0.7824 (p90) cc_final: 0.7371 (p-90) REVERT: b 284 MET cc_start: 0.8320 (ptp) cc_final: 0.7889 (ptp) REVERT: b 311 ASP cc_start: 0.9018 (m-30) cc_final: 0.8460 (m-30) REVERT: b 333 SER cc_start: 0.9320 (p) cc_final: 0.9034 (m) REVERT: b 371 TYR cc_start: 0.7511 (m-80) cc_final: 0.7257 (m-80) REVERT: b 408 ASP cc_start: 0.7617 (t0) cc_final: 0.7338 (t70) REVERT: b 410 MET cc_start: 0.9008 (mtt) cc_final: 0.8719 (mtp) REVERT: C 75 MET cc_start: 0.8206 (mmt) cc_final: 0.7704 (mmt) REVERT: C 96 MET cc_start: 0.7898 (ppp) cc_final: 0.7118 (ppp) REVERT: C 116 LYS cc_start: 0.8178 (mttt) cc_final: 0.7489 (tptt) REVERT: C 134 MET cc_start: 0.7315 (ttp) cc_final: 0.6064 (mtt) REVERT: C 227 TRP cc_start: 0.7431 (p90) cc_final: 0.7032 (p-90) REVERT: c 284 MET cc_start: 0.7514 (pmm) cc_final: 0.7248 (pmm) REVERT: c 311 ASP cc_start: 0.9051 (m-30) cc_final: 0.8627 (m-30) REVERT: c 321 GLN cc_start: 0.8461 (mt0) cc_final: 0.7891 (mm-40) REVERT: c 325 ARG cc_start: 0.8808 (mpt180) cc_final: 0.7777 (mpt180) REVERT: c 371 TYR cc_start: 0.7528 (m-80) cc_final: 0.7158 (m-80) REVERT: c 410 MET cc_start: 0.8910 (mtt) cc_final: 0.8684 (mtp) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.2461 time to fit residues: 75.7007 Evaluate side-chains 176 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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: 1.9990 chunk 87 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 331 GLN b 338 ASN C 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12231 Z= 0.275 Angle : 0.834 9.674 16650 Z= 0.412 Chirality : 0.048 0.339 2202 Planarity : 0.004 0.050 2070 Dihedral : 10.134 61.389 3336 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -1.33 (0.20), residues: 1605 helix: 0.17 (0.29), residues: 327 sheet: -0.42 (0.28), residues: 327 loop : -1.47 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 370 HIS 0.007 0.001 HIS A 141 PHE 0.015 0.002 PHE B 157 TYR 0.038 0.002 TYR b 393 ARG 0.007 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 221 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.261 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 96 MET cc_start: 0.7826 (ppp) cc_final: 0.7175 (ppp) REVERT: A 228 GLU cc_start: 0.8397 (pm20) cc_final: 0.7867 (pp20) REVERT: A 229 ASP cc_start: 0.7392 (t0) cc_final: 0.7008 (t0) REVERT: a 284 MET cc_start: 0.7781 (pmm) cc_final: 0.7515 (pmm) REVERT: a 311 ASP cc_start: 0.9081 (m-30) cc_final: 0.8591 (m-30) REVERT: a 351 MET cc_start: 0.8880 (mmp) cc_final: 0.8453 (tpp) REVERT: a 372 LEU cc_start: 0.7311 (tp) cc_final: 0.6311 (tp) REVERT: a 410 MET cc_start: 0.9153 (mtp) cc_final: 0.8878 (mtp) REVERT: B 80 MET cc_start: 0.8678 (mtt) cc_final: 0.8428 (mtt) REVERT: B 82 MET cc_start: 0.9021 (ptp) cc_final: 0.8433 (pmm) REVERT: B 96 MET cc_start: 0.8034 (ppp) cc_final: 0.7353 (ppp) REVERT: B 217 TYR cc_start: 0.7901 (m-80) cc_final: 0.7463 (m-80) REVERT: B 227 TRP cc_start: 0.7816 (p90) cc_final: 0.7580 (p-90) REVERT: b 284 MET cc_start: 0.8246 (ptp) cc_final: 0.7964 (ptp) REVERT: b 311 ASP cc_start: 0.8933 (m-30) cc_final: 0.8441 (m-30) REVERT: b 371 TYR cc_start: 0.7320 (m-80) cc_final: 0.7087 (m-80) REVERT: b 410 MET cc_start: 0.8994 (mtt) cc_final: 0.8659 (mtp) REVERT: C 96 MET cc_start: 0.7908 (ppp) cc_final: 0.7236 (ppp) REVERT: C 116 LYS cc_start: 0.8128 (mttt) cc_final: 0.7439 (tptt) REVERT: C 134 MET cc_start: 0.7234 (ttp) cc_final: 0.5966 (mtt) REVERT: c 284 MET cc_start: 0.7584 (pmm) cc_final: 0.7220 (pmm) REVERT: c 311 ASP cc_start: 0.8998 (m-30) cc_final: 0.8589 (m-30) REVERT: c 321 GLN cc_start: 0.8440 (mt0) cc_final: 0.7806 (mm-40) REVERT: c 325 ARG cc_start: 0.8748 (mpt180) cc_final: 0.7645 (mpt180) REVERT: c 333 SER cc_start: 0.9331 (p) cc_final: 0.9078 (m) REVERT: c 410 MET cc_start: 0.8784 (mtt) cc_final: 0.8448 (mtt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2487 time to fit residues: 77.4981 Evaluate side-chains 178 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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: 40.0000 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 50.0000 chunk 104 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 139 optimal weight: 30.0000 chunk 146 optimal weight: 30.0000 overall best weight: 5.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12231 Z= 0.420 Angle : 0.961 9.845 16650 Z= 0.478 Chirality : 0.051 0.339 2202 Planarity : 0.005 0.051 2070 Dihedral : 10.785 62.841 3336 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: -1.98 (0.19), residues: 1605 helix: -0.57 (0.26), residues: 327 sheet: -0.87 (0.26), residues: 336 loop : -1.80 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 210 HIS 0.016 0.002 HIS C 230 PHE 0.035 0.003 PHE C 157 TYR 0.028 0.003 TYR b 393 ARG 0.008 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 207 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9316 (mp) cc_final: 0.9040 (mp) REVERT: A 94 TYR cc_start: 0.8084 (p90) cc_final: 0.7726 (p90) REVERT: A 96 MET cc_start: 0.8101 (ppp) cc_final: 0.7460 (ppp) REVERT: a 284 MET cc_start: 0.7660 (pmm) cc_final: 0.7270 (pmm) REVERT: a 311 ASP cc_start: 0.9129 (m-30) cc_final: 0.8634 (m-30) REVERT: a 351 MET cc_start: 0.9062 (mmp) cc_final: 0.8615 (tpp) REVERT: a 410 MET cc_start: 0.9053 (mtp) cc_final: 0.8846 (mtp) REVERT: B 80 MET cc_start: 0.8836 (mtt) cc_final: 0.8593 (mtt) REVERT: B 96 MET cc_start: 0.8124 (ppp) cc_final: 0.7468 (ppp) REVERT: B 217 TYR cc_start: 0.8088 (m-80) cc_final: 0.7587 (m-80) REVERT: B 227 TRP cc_start: 0.7907 (p90) cc_final: 0.7684 (p-90) REVERT: b 284 MET cc_start: 0.8097 (ptp) cc_final: 0.7722 (ptp) REVERT: b 311 ASP cc_start: 0.8965 (m-30) cc_final: 0.8408 (m-30) REVERT: b 371 TYR cc_start: 0.7676 (m-80) cc_final: 0.7282 (m-80) REVERT: b 410 MET cc_start: 0.8888 (mtt) cc_final: 0.8555 (mtt) REVERT: C 80 MET cc_start: 0.8949 (mtm) cc_final: 0.8515 (mmt) REVERT: C 82 MET cc_start: 0.9208 (ptp) cc_final: 0.8949 (ptp) REVERT: C 94 TYR cc_start: 0.8269 (p90) cc_final: 0.8043 (p90) REVERT: C 96 MET cc_start: 0.8114 (ppp) cc_final: 0.7319 (ppp) REVERT: C 116 LYS cc_start: 0.8135 (mttt) cc_final: 0.7433 (tptt) REVERT: C 134 MET cc_start: 0.7393 (ttp) cc_final: 0.6134 (mtt) REVERT: C 200 TYR cc_start: 0.8608 (p90) cc_final: 0.8212 (p90) REVERT: c 284 MET cc_start: 0.7849 (pmm) cc_final: 0.7369 (pmm) REVERT: c 311 ASP cc_start: 0.8946 (m-30) cc_final: 0.8506 (m-30) REVERT: c 321 GLN cc_start: 0.8475 (mt0) cc_final: 0.7937 (mm-40) REVERT: c 325 ARG cc_start: 0.8838 (mpt180) cc_final: 0.7757 (mpt180) REVERT: c 410 MET cc_start: 0.8901 (mtt) cc_final: 0.8645 (mtp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2557 time to fit residues: 74.4161 Evaluate side-chains 166 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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: 5.9990 chunk 142 optimal weight: 0.0970 chunk 146 optimal weight: 30.0000 chunk 85 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 151 optimal weight: 0.0980 overall best weight: 3.4384 ------------------------------------------------------------------------------- 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** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12231 Z= 0.312 Angle : 0.884 9.941 16650 Z= 0.438 Chirality : 0.050 0.375 2202 Planarity : 0.004 0.050 2070 Dihedral : 10.476 59.319 3336 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.20), residues: 1605 helix: -0.35 (0.27), residues: 327 sheet: -1.03 (0.26), residues: 333 loop : -1.66 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 227 HIS 0.009 0.002 HIS C 230 PHE 0.026 0.002 PHE C 191 TYR 0.027 0.003 TYR a 366 ARG 0.007 0.001 ARG B 193 *********************** 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 213 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.394 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 94 TYR cc_start: 0.8056 (p90) cc_final: 0.7716 (p90) REVERT: A 96 MET cc_start: 0.8020 (ppp) cc_final: 0.7355 (ppp) REVERT: A 228 GLU cc_start: 0.8474 (pm20) cc_final: 0.7689 (pp20) REVERT: A 229 ASP cc_start: 0.7885 (t0) cc_final: 0.7512 (t0) REVERT: a 284 MET cc_start: 0.7747 (pmm) cc_final: 0.7336 (pmm) REVERT: a 311 ASP cc_start: 0.9135 (m-30) cc_final: 0.8587 (m-30) REVERT: a 351 MET cc_start: 0.8965 (mmp) cc_final: 0.8630 (tpp) REVERT: B 82 MET cc_start: 0.8831 (ptp) cc_final: 0.8212 (pmm) REVERT: B 96 MET cc_start: 0.8135 (ppp) cc_final: 0.7472 (ppp) REVERT: b 284 MET cc_start: 0.8123 (ptp) cc_final: 0.7852 (ptp) REVERT: b 311 ASP cc_start: 0.8926 (m-30) cc_final: 0.8358 (m-30) REVERT: b 335 GLN cc_start: 0.9135 (pm20) cc_final: 0.8852 (pm20) REVERT: b 339 LYS cc_start: 0.9344 (mptt) cc_final: 0.9076 (mppt) REVERT: b 363 TYR cc_start: 0.7857 (p90) cc_final: 0.7612 (p90) REVERT: C 80 MET cc_start: 0.8903 (mtm) cc_final: 0.8427 (mmt) REVERT: C 94 TYR cc_start: 0.8269 (p90) cc_final: 0.7947 (p90) REVERT: C 96 MET cc_start: 0.8161 (ppp) cc_final: 0.7394 (ppp) REVERT: C 116 LYS cc_start: 0.8155 (mttt) cc_final: 0.7451 (tptt) REVERT: C 134 MET cc_start: 0.7458 (ttp) cc_final: 0.6255 (mtt) REVERT: C 200 TYR cc_start: 0.8521 (p90) cc_final: 0.8204 (p90) REVERT: C 236 PRO cc_start: 0.9141 (Cg_endo) cc_final: 0.8936 (Cg_exo) REVERT: c 284 MET cc_start: 0.7817 (pmm) cc_final: 0.7406 (pmm) REVERT: c 311 ASP cc_start: 0.8953 (m-30) cc_final: 0.8521 (m-30) REVERT: c 321 GLN cc_start: 0.8487 (mt0) cc_final: 0.7886 (mm-40) REVERT: c 325 ARG cc_start: 0.8771 (mpt180) cc_final: 0.7629 (mpt180) REVERT: c 410 MET cc_start: 0.8885 (mtt) cc_final: 0.8627 (mtp) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2470 time to fit residues: 74.2671 Evaluate side-chains 170 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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: 10.0000 chunk 71 optimal weight: 0.0970 chunk 104 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 97 optimal weight: 50.0000 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 40.0000 chunk 134 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.7077 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= 0.253 Angle : 0.824 10.003 16650 Z= 0.405 Chirality : 0.048 0.339 2202 Planarity : 0.004 0.051 2070 Dihedral : 9.909 59.998 3336 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.20), residues: 1605 helix: -0.14 (0.28), residues: 330 sheet: -0.96 (0.26), residues: 336 loop : -1.60 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 210 HIS 0.007 0.001 HIS B 230 PHE 0.020 0.002 PHE A 233 TYR 0.024 0.002 TYR b 393 ARG 0.008 0.001 ARG C 193 ********************** 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 217 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.248 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 75 MET cc_start: 0.8353 (mmp) cc_final: 0.7502 (mmt) REVERT: A 96 MET cc_start: 0.7903 (ppp) cc_final: 0.7258 (ppp) REVERT: A 161 LYS cc_start: 0.8373 (pttt) cc_final: 0.8056 (pttp) REVERT: A 228 GLU cc_start: 0.8482 (pm20) cc_final: 0.7628 (pp20) REVERT: A 229 ASP cc_start: 0.7731 (t0) cc_final: 0.7296 (t0) REVERT: a 284 MET cc_start: 0.7676 (pmm) cc_final: 0.7273 (pmm) REVERT: a 311 ASP cc_start: 0.9060 (m-30) cc_final: 0.8507 (m-30) REVERT: a 345 ILE cc_start: 0.8584 (pt) cc_final: 0.8375 (pt) REVERT: a 351 MET cc_start: 0.8919 (mmp) cc_final: 0.8530 (tpp) REVERT: B 76 GLU cc_start: 0.8918 (tp30) cc_final: 0.8612 (tp30) REVERT: B 96 MET cc_start: 0.7987 (ppp) cc_final: 0.7366 (ppp) REVERT: b 284 MET cc_start: 0.8143 (ptp) cc_final: 0.7861 (ptp) REVERT: b 311 ASP cc_start: 0.8837 (m-30) cc_final: 0.8278 (m-30) REVERT: b 363 TYR cc_start: 0.7791 (p90) cc_final: 0.7480 (p90) REVERT: C 80 MET cc_start: 0.8920 (mtm) cc_final: 0.8430 (mmt) REVERT: C 94 TYR cc_start: 0.8230 (p90) cc_final: 0.7943 (p90) REVERT: C 96 MET cc_start: 0.8074 (ppp) cc_final: 0.7301 (ppp) REVERT: C 116 LYS cc_start: 0.8124 (mttt) cc_final: 0.7401 (tptt) REVERT: C 134 MET cc_start: 0.7431 (ttp) cc_final: 0.6246 (mtt) REVERT: C 142 LEU cc_start: 0.9147 (pp) cc_final: 0.8876 (mm) REVERT: C 200 TYR cc_start: 0.8426 (p90) cc_final: 0.8156 (p90) REVERT: c 284 MET cc_start: 0.7905 (pmm) cc_final: 0.7447 (pmm) REVERT: c 311 ASP cc_start: 0.8980 (m-30) cc_final: 0.8663 (m-30) REVERT: c 321 GLN cc_start: 0.8433 (mt0) cc_final: 0.7838 (mm-40) REVERT: c 410 MET cc_start: 0.8846 (mtt) cc_final: 0.8590 (mtp) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2388 time to fit residues: 73.7102 Evaluate side-chains 173 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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: 20.0000 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 40.0000 chunk 126 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- 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** B 141 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.072270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.061419 restraints weight = 80818.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062672 restraints weight = 53310.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063550 restraints weight = 39850.659| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.7255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12231 Z= 0.303 Angle : 0.849 9.932 16650 Z= 0.420 Chirality : 0.049 0.328 2202 Planarity : 0.005 0.065 2070 Dihedral : 9.916 58.381 3336 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -1.86 (0.20), residues: 1605 helix: -0.37 (0.27), residues: 330 sheet: -1.08 (0.26), residues: 333 loop : -1.64 (0.19), residues: 942 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 0.018 0.002 PHE A 233 TYR 0.029 0.003 TYR a 371 ARG 0.008 0.001 ARG B 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.71 seconds wall clock time: 45 minutes 33.46 seconds (2733.46 seconds total)