Starting phenix.real_space_refine on Tue Apr 9 17:08:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ken_8242/04_2024/5ken_8242.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ken_8242/04_2024/5ken_8242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ken_8242/04_2024/5ken_8242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ken_8242/04_2024/5ken_8242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ken_8242/04_2024/5ken_8242.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ken_8242/04_2024/5ken_8242.pdb" } resolution = 4.3 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= 0.002 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 71 5.16 5 C 10701 2.51 5 N 2796 2.21 5 O 3345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 614": "OD1" <-> "OD2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 305": "OE1" <-> "OE2" Residue "M TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16913 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1596 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "C" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 903 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "D" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1829 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 903 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1829 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "N" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 903 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "O" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "P" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "Q" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.38, per 1000 atoms: 0.55 Number of scatterers: 16913 At special positions: 0 Unit cell: (154.58, 141.48, 149.34, 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 71 16.00 O 3345 8.00 N 2796 7.00 C 10701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=2.06 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.02 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.02 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.09 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.07 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.08 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS M 609 " distance=2.04 Simple disulfide: pdb=" SG CYS K 108 " - pdb=" SG CYS K 135 " distance=2.02 Simple disulfide: pdb=" SG CYS K 121 " - pdb=" SG CYS K 147 " distance=2.02 Simple disulfide: pdb=" SG CYS M 511 " - pdb=" SG CYS M 556 " distance=2.04 Simple disulfide: pdb=" SG CYS M 601 " - pdb=" SG CYS M 608 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.10 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.12 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " 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 Atom "HETATM16827 O5 NAG U 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA L 3 " - " MAN L 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA L 3 " - " MAN L 5 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG E 401 " - " ASN E 238 " " NAG K 407 " - " ASN K 238 " " NAG S 1 " - " ASN F 563 " " NAG T 1 " - " ASN M 563 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.36 Conformation dependent library (CDL) restraints added in 3.0 seconds 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3884 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 35 sheets defined 16.9% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.593A pdb=" N TRP B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 536 Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'C' and resid 26 through 32 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'F' and resid 527 through 532 removed outlier: 3.549A pdb=" N TRP F 531 " --> pdb=" O ILE F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.517A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'G' and resid 26 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 86 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 60 through 65 removed outlier: 4.290A pdb=" N SER J 65 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 59 through 61 No H-bonds generated for 'chain 'K' and resid 59 through 61' Processing helix chain 'K' and resid 71 through 74 Processing helix chain 'K' and resid 78 through 85 Processing helix chain 'K' and resid 210 through 215 Processing helix chain 'K' and resid 249 through 256 Processing helix chain 'K' and resid 257 through 260 Processing helix chain 'M' and resid 527 through 532 removed outlier: 3.595A pdb=" N TRP M 531 " --> pdb=" O ILE M 527 " (cutoff:3.500A) Processing helix chain 'M' and resid 533 through 536 Processing helix chain 'M' and resid 538 through 543 removed outlier: 3.705A pdb=" N ILE M 542 " --> pdb=" O ALA M 539 " (cutoff:3.500A) Processing helix chain 'M' and resid 553 through 576 removed outlier: 3.555A pdb=" N GLY M 557 " --> pdb=" O GLY M 553 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN M 567 " --> pdb=" O ASN M 563 " (cutoff:3.500A) Processing helix chain 'M' and resid 584 through 597 Processing helix chain 'N' and resid 26 through 32 removed outlier: 3.573A pdb=" N PHE N 29 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 75 No H-bonds generated for 'chain 'N' and resid 73 through 75' Processing helix chain 'N' and resid 83 through 86 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 40 through 43 Processing helix chain 'Q' and resid 60 through 65 removed outlier: 4.357A pdb=" N SER Q 65 " --> pdb=" O PRO Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 75 No H-bonds generated for 'chain 'Q' and resid 73 through 75' Processing helix chain 'Q' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.890A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 4.053A pdb=" N GLU A 103 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 111 removed outlier: 8.393A pdb=" N ALA A 105 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 138 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASN A 107 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N LYS A 140 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR A 109 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N SER A 142 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N LEU A 111 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N THR A 144 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.209A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.227A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.838A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AB1, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'E' and resid 105 through 111 removed outlier: 6.516A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.131A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.324A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.396A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.111A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 8 removed outlier: 5.097A pdb=" N GLY J 16 " --> pdb=" O ASN J 82B" (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.385A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.385A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 42 through 45 removed outlier: 6.573A pdb=" N GLY K 36 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 67 through 69 Processing sheet with id=AC6, first strand: chain 'K' and resid 102 through 103 Processing sheet with id=AC7, first strand: chain 'K' and resid 107 through 111 removed outlier: 6.499A pdb=" N CYS K 108 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL K 141 " --> pdb=" O CYS K 108 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN K 110 " --> pdb=" O VAL K 141 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLY K 143 " --> pdb=" O ASN K 110 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TYR K 220 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS K 140 " --> pdb=" O TYR K 220 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA K 222 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER K 142 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG K 219 " --> pdb=" O GLU K 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.370A pdb=" N GLU N 10 " --> pdb=" O THR N 110 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'O' and resid 10 through 13 removed outlier: 5.908A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.780A pdb=" N VAL P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 10 through 13 removed outlier: 4.224A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 4 through 7 removed outlier: 5.462A pdb=" N GLY Q 16 " --> pdb=" O ASN Q 82B" (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 56 through 59 removed outlier: 5.269A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 56 through 59 removed outlier: 5.269A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.23 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3906 1.32 - 1.45: 4815 1.45 - 1.57: 8489 1.57 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 17302 Sorted by residual: bond pdb=" CA LEU F 569 " pdb=" C LEU F 569 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.26e-02 6.30e+03 1.89e+01 bond pdb=" CA LEU F 515 " pdb=" C LEU F 515 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.20e-02 6.94e+03 1.73e+01 bond pdb=" CA LEU M 569 " pdb=" C LEU M 569 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.26e-02 6.30e+03 1.69e+01 bond pdb=" CA ILE K 301 " pdb=" C ILE K 301 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" CA LEU B 569 " pdb=" C LEU B 569 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.27e-02 6.20e+03 1.54e+01 ... (remaining 17297 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.12: 399 105.12 - 112.36: 8274 112.36 - 119.59: 6596 119.59 - 126.83: 7992 126.83 - 134.07: 222 Bond angle restraints: 23483 Sorted by residual: angle pdb=" C ALA E 125 " pdb=" N PRO E 126 " pdb=" CA PRO E 126 " ideal model delta sigma weight residual 120.03 129.90 -9.87 9.90e-01 1.02e+00 9.95e+01 angle pdb=" C PRO A 93 " pdb=" N PRO A 94 " pdb=" CA PRO A 94 " ideal model delta sigma weight residual 119.85 129.62 -9.77 1.01e+00 9.80e-01 9.36e+01 angle pdb=" C ALA K 125 " pdb=" N PRO K 126 " pdb=" CA PRO K 126 " ideal model delta sigma weight residual 120.03 129.43 -9.40 9.90e-01 1.02e+00 9.02e+01 angle pdb=" C ALA A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta sigma weight residual 120.03 129.38 -9.35 9.90e-01 1.02e+00 8.92e+01 angle pdb=" C PRO K 93 " pdb=" N PRO K 94 " pdb=" CA PRO K 94 " ideal model delta sigma weight residual 119.85 129.34 -9.49 1.01e+00 9.80e-01 8.84e+01 ... (remaining 23478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 10057 21.20 - 42.39: 270 42.39 - 63.59: 97 63.59 - 84.78: 52 84.78 - 105.98: 19 Dihedral angle restraints: 10495 sinusoidal: 4384 harmonic: 6111 Sorted by residual: dihedral pdb=" CB CYS E 53 " pdb=" SG CYS E 53 " pdb=" SG CYS F 609 " pdb=" CB CYS F 609 " ideal model delta sinusoidal sigma weight residual -86.00 -170.44 84.44 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CA MET J 100D" pdb=" C MET J 100D" pdb=" N GLY J 101 " pdb=" CA GLY J 101 " ideal model delta harmonic sigma weight residual 0.00 44.34 -44.34 0 5.00e+00 4.00e-02 7.86e+01 dihedral pdb=" CB CYS M 601 " pdb=" SG CYS M 601 " pdb=" SG CYS M 608 " pdb=" CB CYS M 608 " ideal model delta sinusoidal sigma weight residual 93.00 168.96 -75.96 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 10492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.445: 2633 1.445 - 2.890: 0 2.890 - 4.335: 0 4.335 - 5.780: 1 5.780 - 7.226: 1 Chirality restraints: 2635 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN M 563 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 4.83 -7.23 2.00e-01 2.50e+01 1.31e+03 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 2.67 -5.07 2.00e-01 2.50e+01 6.42e+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 -2.22 -0.18 2.00e-02 2.50e+03 8.42e+01 ... (remaining 2632 not shown) Planarity restraints: 2991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN M 563 " 0.372 2.00e-02 2.50e+03 5.32e-01 3.53e+03 pdb=" CG ASN M 563 " -0.188 2.00e-02 2.50e+03 pdb=" OD1 ASN M 563 " -0.940 2.00e-02 2.50e+03 pdb=" ND2 ASN M 563 " 0.188 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " 0.568 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 238 " 0.252 2.00e-02 2.50e+03 3.93e-01 1.93e+03 pdb=" CG ASN E 238 " -0.168 2.00e-02 2.50e+03 pdb=" OD1 ASN E 238 " -0.599 2.00e-02 2.50e+03 pdb=" ND2 ASN E 238 " -0.049 2.00e-02 2.50e+03 pdb=" C1 NAG E 401 " 0.565 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 563 " 0.263 2.00e-02 2.50e+03 3.33e-01 1.39e+03 pdb=" CG ASN F 563 " -0.151 2.00e-02 2.50e+03 pdb=" OD1 ASN F 563 " -0.453 2.00e-02 2.50e+03 pdb=" ND2 ASN F 563 " -0.145 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.486 2.00e-02 2.50e+03 ... (remaining 2988 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 11 2.01 - 2.73: 2275 2.73 - 3.45: 24857 3.45 - 4.18: 45430 4.18 - 4.90: 76778 Nonbonded interactions: 149351 Sorted by model distance: nonbonded pdb=" OE1 GLU K 156 " pdb=" O3 NAG T 1 " model vdw 1.282 2.440 nonbonded pdb=" OD1 ASN E 238 " pdb=" C1 NAG E 401 " model vdw 1.375 2.776 nonbonded pdb=" OD1 ASN F 563 " pdb=" C1 NAG S 1 " model vdw 1.376 2.776 nonbonded pdb=" ND2 ASN E 257 " pdb=" C7 NAG R 1 " model vdw 1.412 3.350 nonbonded pdb=" ND2 ASN E 257 " pdb=" N2 NAG R 1 " model vdw 1.478 3.200 ... (remaining 149346 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 'E' and resid 33 through 260) selection = (chain 'K' and resid 33 through 260) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'R' selection = chain 'U' selection = chain 'V' } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.100 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 48.180 Find NCS groups from input model: 1.160 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.014 0.064 17302 Z= 0.898 Angle : 1.820 10.902 23483 Z= 1.211 Chirality : 0.194 7.226 2635 Planarity : 0.013 0.161 2987 Dihedral : 13.218 105.976 6536 Min Nonbonded Distance : 1.282 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 1.43 % Allowed : 2.95 % Favored : 95.63 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.55 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.45 (0.18), residues: 2105 helix: -1.18 (0.30), residues: 189 sheet: 0.26 (0.19), residues: 622 loop : 1.97 (0.19), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.012 TRP F 597 HIS 0.007 0.002 HIS E 39 PHE 0.041 0.006 PHE A 176 TYR 0.071 0.009 TYR M 534 ARG 0.006 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 352 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 132 PHE cc_start: 0.8188 (t80) cc_final: 0.7779 (t80) REVERT: B 561 LEU cc_start: 0.9580 (tp) cc_final: 0.9096 (tp) REVERT: B 603 ILE cc_start: 0.5059 (mt) cc_final: 0.3347 (tt) REVERT: C 59 TYR cc_start: 0.9371 (p90) cc_final: 0.9062 (p90) REVERT: C 86 ASP cc_start: 0.8799 (m-30) cc_final: 0.7746 (m-30) REVERT: D 11 LEU cc_start: 0.9124 (tp) cc_final: 0.8764 (tp) REVERT: D 21 ILE cc_start: 0.9307 (mt) cc_final: 0.8982 (tp) REVERT: D 73 LEU cc_start: 0.9361 (tp) cc_final: 0.9073 (tp) REVERT: D 87 PHE cc_start: 0.9371 (m-80) cc_final: 0.9113 (m-10) REVERT: E 120 GLU cc_start: 0.8119 (tt0) cc_final: 0.7867 (tp30) REVERT: E 171 TYR cc_start: 0.9009 (m-80) cc_final: 0.8299 (m-80) REVERT: E 183 PHE cc_start: 0.9219 (m-80) cc_final: 0.8967 (m-80) REVERT: F 603 ILE cc_start: 0.7638 (mt) cc_final: 0.5261 (mt) REVERT: G 82 LEU cc_start: 0.8979 (mt) cc_final: 0.8521 (mt) REVERT: G 90 TYR cc_start: 0.9070 (m-80) cc_final: 0.8792 (m-80) REVERT: H 39 LYS cc_start: 0.9362 (mmmt) cc_final: 0.8824 (mmpt) REVERT: H 61 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8359 (mtm-85) REVERT: H 73 LEU cc_start: 0.9295 (tp) cc_final: 0.8853 (tp) REVERT: H 78 LEU cc_start: 0.9374 (tp) cc_final: 0.9122 (tp) REVERT: H 86 TYR cc_start: 0.8378 (m-80) cc_final: 0.8014 (m-80) REVERT: H 87 PHE cc_start: 0.8622 (m-80) cc_final: 0.7808 (m-80) REVERT: I 85 ASP cc_start: 0.9325 (m-30) cc_final: 0.8948 (t0) REVERT: J 27 PHE cc_start: 0.7795 (t80) cc_final: 0.7485 (t80) REVERT: J 63 LEU cc_start: 0.8791 (mt) cc_final: 0.8486 (pp) REVERT: N 109 VAL cc_start: 0.9230 (t) cc_final: 0.8681 (t) REVERT: O 21 ILE cc_start: 0.9505 (mt) cc_final: 0.9270 (tp) REVERT: O 30 TYR cc_start: 0.8383 (m-80) cc_final: 0.7896 (m-80) outliers start: 4 outliers final: 2 residues processed: 356 average time/residue: 0.3674 time to fit residues: 184.7538 Evaluate side-chains 186 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 161 optimal weight: 0.0270 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 overall best weight: 3.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN B 551 GLN ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN K 39 HIS K 221 GLN K 268 ASN ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17302 Z= 0.288 Angle : 0.791 9.116 23483 Z= 0.433 Chirality : 0.047 0.274 2635 Planarity : 0.006 0.100 2987 Dihedral : 11.430 83.337 2807 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.95 % Allowed : 4.09 % Favored : 94.96 % Rotamer: Outliers : 0.06 % Allowed : 1.34 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2105 helix: -0.85 (0.35), residues: 190 sheet: -0.61 (0.19), residues: 601 loop : 0.96 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 531 HIS 0.008 0.001 HIS O 91 PHE 0.028 0.003 PHE Q 98 TYR 0.031 0.002 TYR A 137 ARG 0.008 0.001 ARG K 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8650 (t80) cc_final: 0.7479 (t80) REVERT: B 578 GLU cc_start: 0.8824 (pt0) cc_final: 0.8595 (pt0) REVERT: B 603 ILE cc_start: 0.6558 (mt) cc_final: 0.5769 (tt) REVERT: C 59 TYR cc_start: 0.9406 (p90) cc_final: 0.9173 (p90) REVERT: C 86 ASP cc_start: 0.8452 (m-30) cc_final: 0.8074 (m-30) REVERT: D 21 ILE cc_start: 0.9310 (mt) cc_final: 0.9055 (tp) REVERT: E 120 GLU cc_start: 0.8405 (tt0) cc_final: 0.7992 (tp30) REVERT: E 171 TYR cc_start: 0.8981 (m-80) cc_final: 0.8151 (m-80) REVERT: E 183 PHE cc_start: 0.9238 (m-80) cc_final: 0.8960 (m-80) REVERT: E 301 ILE cc_start: 0.6028 (mm) cc_final: 0.5351 (mm) REVERT: F 595 GLN cc_start: 0.9452 (tm-30) cc_final: 0.9224 (tm-30) REVERT: G 90 TYR cc_start: 0.8910 (m-80) cc_final: 0.8661 (m-80) REVERT: G 97 TYR cc_start: 0.2513 (m-80) cc_final: 0.2228 (m-80) REVERT: H 39 LYS cc_start: 0.9279 (mmmt) cc_final: 0.9035 (ttpp) REVERT: H 87 PHE cc_start: 0.8676 (m-80) cc_final: 0.8473 (m-80) REVERT: I 85 ASP cc_start: 0.9321 (m-30) cc_final: 0.8999 (p0) REVERT: I 94 TYR cc_start: 0.9104 (p90) cc_final: 0.8801 (p90) REVERT: J 53 TRP cc_start: 0.8509 (t-100) cc_final: 0.7884 (t-100) REVERT: M 595 GLN cc_start: 0.9760 (tp40) cc_final: 0.9476 (tm-30) REVERT: N 90 TYR cc_start: 0.8850 (m-10) cc_final: 0.8621 (m-80) REVERT: N 109 VAL cc_start: 0.9356 (t) cc_final: 0.8864 (t) REVERT: O 21 ILE cc_start: 0.9416 (mt) cc_final: 0.9164 (tp) REVERT: Q 43 LYS cc_start: 0.9148 (mmpt) cc_final: 0.8807 (ptmm) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.3450 time to fit residues: 123.7422 Evaluate side-chains 156 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 20.0000 chunk 58 optimal weight: 0.0060 chunk 155 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 202 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 overall best weight: 4.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17302 Z= 0.294 Angle : 0.751 12.486 23483 Z= 0.406 Chirality : 0.045 0.246 2635 Planarity : 0.005 0.079 2987 Dihedral : 10.257 79.116 2807 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.56 % Favored : 93.73 % Rotamer: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2105 helix: -1.23 (0.33), residues: 190 sheet: -0.91 (0.19), residues: 613 loop : 0.47 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 531 HIS 0.011 0.002 HIS O 91 PHE 0.020 0.002 PHE Q 98 TYR 0.027 0.002 TYR A 137 ARG 0.008 0.001 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8705 (t80) cc_final: 0.8444 (t80) REVERT: B 578 GLU cc_start: 0.9000 (pt0) cc_final: 0.8679 (pt0) REVERT: C 59 TYR cc_start: 0.9416 (p90) cc_final: 0.9127 (p90) REVERT: C 86 ASP cc_start: 0.8536 (m-30) cc_final: 0.8162 (m-30) REVERT: D 11 LEU cc_start: 0.9307 (tp) cc_final: 0.8948 (tt) REVERT: D 21 ILE cc_start: 0.9417 (mt) cc_final: 0.9151 (tp) REVERT: E 120 GLU cc_start: 0.8675 (tt0) cc_final: 0.8301 (tt0) REVERT: E 171 TYR cc_start: 0.9019 (m-80) cc_final: 0.8166 (m-80) REVERT: E 183 PHE cc_start: 0.9107 (m-80) cc_final: 0.8837 (m-80) REVERT: E 301 ILE cc_start: 0.6127 (mm) cc_final: 0.5881 (mm) REVERT: F 595 GLN cc_start: 0.9526 (tm-30) cc_final: 0.9174 (tm-30) REVERT: G 34 MET cc_start: 0.9368 (mmm) cc_final: 0.8652 (mmm) REVERT: G 36 TRP cc_start: 0.8365 (m100) cc_final: 0.7973 (m100) REVERT: G 90 TYR cc_start: 0.8774 (m-80) cc_final: 0.8500 (m-80) REVERT: H 39 LYS cc_start: 0.9321 (mmmt) cc_final: 0.9044 (pttp) REVERT: H 96 PHE cc_start: 0.8918 (m-10) cc_final: 0.8714 (m-10) REVERT: I 38 GLN cc_start: 0.9149 (tt0) cc_final: 0.8906 (tt0) REVERT: I 85 ASP cc_start: 0.9397 (m-30) cc_final: 0.9088 (p0) REVERT: J 18 LEU cc_start: 0.8473 (tp) cc_final: 0.8060 (tp) REVERT: J 53 TRP cc_start: 0.8564 (t-100) cc_final: 0.8014 (t-100) REVERT: M 595 GLN cc_start: 0.9765 (tp40) cc_final: 0.9471 (tm-30) REVERT: N 90 TYR cc_start: 0.8930 (m-10) cc_final: 0.8568 (m-10) REVERT: N 109 VAL cc_start: 0.9500 (t) cc_final: 0.8892 (t) REVERT: Q 53 TRP cc_start: 0.7251 (m100) cc_final: 0.6885 (m100) outliers start: 2 outliers final: 2 residues processed: 207 average time/residue: 0.3356 time to fit residues: 101.4077 Evaluate side-chains 143 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 97 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 53 optimal weight: 30.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN G 39 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN K 278 ASN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17302 Z= 0.234 Angle : 0.675 10.660 23483 Z= 0.363 Chirality : 0.044 0.240 2635 Planarity : 0.005 0.068 2987 Dihedral : 9.588 80.636 2807 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.70 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.49 (0.19), residues: 2105 helix: -0.99 (0.35), residues: 181 sheet: -0.98 (0.20), residues: 611 loop : 0.26 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 531 HIS 0.006 0.001 HIS O 91 PHE 0.020 0.002 PHE O 71 TYR 0.022 0.002 TYR A 137 ARG 0.011 0.001 ARG E 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8755 (t80) cc_final: 0.8500 (t80) REVERT: B 578 GLU cc_start: 0.9002 (pt0) cc_final: 0.8699 (pt0) REVERT: C 59 TYR cc_start: 0.9406 (p90) cc_final: 0.9129 (p90) REVERT: C 86 ASP cc_start: 0.8570 (m-30) cc_final: 0.8190 (m-30) REVERT: C 102 TYR cc_start: 0.8837 (p90) cc_final: 0.8622 (p90) REVERT: D 11 LEU cc_start: 0.9308 (tp) cc_final: 0.8995 (tt) REVERT: D 21 ILE cc_start: 0.9433 (mt) cc_final: 0.9180 (tp) REVERT: E 120 GLU cc_start: 0.8718 (tt0) cc_final: 0.8333 (tt0) REVERT: E 171 TYR cc_start: 0.9017 (m-80) cc_final: 0.8089 (m-80) REVERT: F 595 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9077 (tm-30) REVERT: G 34 MET cc_start: 0.9310 (mmm) cc_final: 0.8003 (mmm) REVERT: G 36 TRP cc_start: 0.8721 (m100) cc_final: 0.8511 (m100) REVERT: H 39 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9090 (pttp) REVERT: H 61 ARG cc_start: 0.8965 (mtm-85) cc_final: 0.7987 (ptt-90) REVERT: H 73 LEU cc_start: 0.9163 (tp) cc_final: 0.8922 (tp) REVERT: H 79 GLN cc_start: 0.9534 (mm-40) cc_final: 0.9184 (mp10) REVERT: H 96 PHE cc_start: 0.8876 (m-10) cc_final: 0.8591 (m-10) REVERT: J 53 TRP cc_start: 0.8429 (t-100) cc_final: 0.7803 (t-100) REVERT: M 595 GLN cc_start: 0.9760 (tp40) cc_final: 0.9367 (tm-30) REVERT: N 34 MET cc_start: 0.9018 (tpt) cc_final: 0.8803 (tpp) REVERT: N 90 TYR cc_start: 0.8922 (m-10) cc_final: 0.8582 (m-10) REVERT: N 109 VAL cc_start: 0.9370 (t) cc_final: 0.8953 (t) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3309 time to fit residues: 95.0818 Evaluate side-chains 134 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BASN K 44 GLN K 73 ASN M 567 GLN M 602 HIS ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100BASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17302 Z= 0.281 Angle : 0.719 9.344 23483 Z= 0.384 Chirality : 0.044 0.258 2635 Planarity : 0.005 0.060 2987 Dihedral : 8.997 84.562 2807 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 30.90 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.79 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 2105 helix: -1.12 (0.36), residues: 172 sheet: -1.07 (0.20), residues: 600 loop : 0.01 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 531 HIS 0.008 0.002 HIS O 91 PHE 0.026 0.002 PHE G 32 TYR 0.027 0.002 TYR N 79 ARG 0.010 0.001 ARG E 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8937 (t80) cc_final: 0.8586 (t80) REVERT: C 59 TYR cc_start: 0.9431 (p90) cc_final: 0.9113 (p90) REVERT: C 102 TYR cc_start: 0.8821 (p90) cc_final: 0.8585 (p90) REVERT: D 11 LEU cc_start: 0.9353 (tp) cc_final: 0.9036 (tt) REVERT: E 51 LEU cc_start: 0.6528 (mt) cc_final: 0.6140 (mt) REVERT: E 171 TYR cc_start: 0.9027 (m-80) cc_final: 0.8170 (m-80) REVERT: F 595 GLN cc_start: 0.9476 (tm-30) cc_final: 0.9006 (tm-30) REVERT: G 34 MET cc_start: 0.9199 (mmm) cc_final: 0.6871 (tpp) REVERT: G 36 TRP cc_start: 0.8949 (m100) cc_final: 0.8270 (m100) REVERT: G 90 TYR cc_start: 0.9066 (m-80) cc_final: 0.8848 (m-80) REVERT: H 73 LEU cc_start: 0.9229 (tp) cc_final: 0.8981 (tp) REVERT: H 79 GLN cc_start: 0.9525 (mm-40) cc_final: 0.9211 (mp10) REVERT: I 85 ASP cc_start: 0.9443 (m-30) cc_final: 0.9106 (t70) REVERT: J 102 TYR cc_start: 0.8849 (t80) cc_final: 0.8380 (t80) REVERT: N 34 MET cc_start: 0.9188 (tpt) cc_final: 0.8909 (tpp) REVERT: N 79 TYR cc_start: 0.9455 (m-10) cc_final: 0.9027 (m-80) REVERT: N 90 TYR cc_start: 0.8944 (m-10) cc_final: 0.8705 (m-10) REVERT: N 98 TYR cc_start: 0.6452 (m-80) cc_final: 0.5923 (m-80) REVERT: P 73 LEU cc_start: 0.9530 (tt) cc_final: 0.9302 (tt) REVERT: Q 53 TRP cc_start: 0.7241 (m100) cc_final: 0.6845 (m100) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3165 time to fit residues: 81.7604 Evaluate side-chains 122 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN D 38 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN H 89 GLN I 37 GLN I 42 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 514 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17302 Z= 0.365 Angle : 0.792 11.348 23483 Z= 0.423 Chirality : 0.046 0.266 2635 Planarity : 0.005 0.054 2987 Dihedral : 9.010 89.072 2807 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 38.85 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.79 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.18), residues: 2105 helix: -1.71 (0.32), residues: 195 sheet: -1.24 (0.19), residues: 667 loop : -0.43 (0.19), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 531 HIS 0.007 0.002 HIS O 91 PHE 0.028 0.003 PHE G 32 TYR 0.023 0.003 TYR E 137 ARG 0.023 0.001 ARG M 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.9005 (t80) cc_final: 0.8654 (t80) REVERT: B 603 ILE cc_start: 0.8315 (tt) cc_final: 0.6970 (tt) REVERT: C 59 TYR cc_start: 0.9467 (p90) cc_final: 0.9075 (p90) REVERT: E 51 LEU cc_start: 0.6619 (mt) cc_final: 0.6220 (mt) REVERT: F 595 GLN cc_start: 0.9472 (tm-30) cc_final: 0.8976 (tm-30) REVERT: G 34 MET cc_start: 0.9203 (mmm) cc_final: 0.7881 (mmm) REVERT: G 36 TRP cc_start: 0.9097 (m100) cc_final: 0.8687 (m100) REVERT: H 38 GLN cc_start: 0.9329 (pm20) cc_final: 0.9086 (pm20) REVERT: H 73 LEU cc_start: 0.9291 (tp) cc_final: 0.9006 (tp) REVERT: I 85 ASP cc_start: 0.9504 (m-30) cc_final: 0.9152 (t70) REVERT: J 102 TYR cc_start: 0.8854 (t80) cc_final: 0.8368 (t80) REVERT: N 13 MET cc_start: 0.9288 (ppp) cc_final: 0.9050 (ppp) REVERT: N 90 TYR cc_start: 0.8924 (m-10) cc_final: 0.8620 (m-80) REVERT: N 109 VAL cc_start: 0.9463 (t) cc_final: 0.8966 (t) REVERT: P 73 LEU cc_start: 0.9579 (tt) cc_final: 0.9355 (tt) REVERT: Q 53 TRP cc_start: 0.7296 (m100) cc_final: 0.6660 (m100) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3041 time to fit residues: 73.0640 Evaluate side-chains 112 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17302 Z= 0.238 Angle : 0.690 13.000 23483 Z= 0.365 Chirality : 0.044 0.246 2635 Planarity : 0.005 0.052 2987 Dihedral : 8.501 82.362 2807 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 31.08 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.79 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.20 (0.19), residues: 2105 helix: -1.20 (0.36), residues: 178 sheet: -1.30 (0.20), residues: 640 loop : -0.35 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP M 531 HIS 0.005 0.001 HIS O 91 PHE 0.021 0.002 PHE G 32 TYR 0.038 0.002 TYR G 90 ARG 0.008 0.001 ARG E 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8969 (t80) cc_final: 0.8644 (t80) REVERT: B 603 ILE cc_start: 0.8542 (tt) cc_final: 0.6444 (tt) REVERT: C 59 TYR cc_start: 0.9489 (p90) cc_final: 0.9096 (p90) REVERT: E 51 LEU cc_start: 0.6656 (mt) cc_final: 0.6225 (mt) REVERT: E 171 TYR cc_start: 0.9050 (m-80) cc_final: 0.8132 (m-80) REVERT: F 595 GLN cc_start: 0.9442 (tm-30) cc_final: 0.8918 (tm-30) REVERT: G 34 MET cc_start: 0.9171 (mmm) cc_final: 0.7460 (mmm) REVERT: G 36 TRP cc_start: 0.9039 (m100) cc_final: 0.8640 (m100) REVERT: H 38 GLN cc_start: 0.9208 (pm20) cc_final: 0.8989 (pm20) REVERT: H 73 LEU cc_start: 0.9216 (tp) cc_final: 0.8918 (tp) REVERT: H 79 GLN cc_start: 0.9549 (mm-40) cc_final: 0.9281 (mp10) REVERT: H 96 PHE cc_start: 0.8827 (m-10) cc_final: 0.8527 (m-10) REVERT: I 85 ASP cc_start: 0.9500 (m-30) cc_final: 0.9152 (t70) REVERT: J 37 PHE cc_start: 0.8478 (p90) cc_final: 0.7916 (p90) REVERT: J 102 TYR cc_start: 0.8794 (t80) cc_final: 0.8351 (t80) REVERT: N 13 MET cc_start: 0.9299 (ppp) cc_final: 0.9080 (ppp) REVERT: N 90 TYR cc_start: 0.8888 (m-10) cc_final: 0.8676 (m-10) REVERT: P 73 LEU cc_start: 0.9561 (tt) cc_final: 0.9319 (tt) REVERT: Q 53 TRP cc_start: 0.7207 (m100) cc_final: 0.6496 (m100) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3016 time to fit residues: 72.2359 Evaluate side-chains 114 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.1980 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17302 Z= 0.189 Angle : 0.657 11.547 23483 Z= 0.345 Chirality : 0.044 0.289 2635 Planarity : 0.004 0.050 2987 Dihedral : 7.975 76.231 2807 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.32 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.15 (0.19), residues: 2105 helix: -0.89 (0.37), residues: 178 sheet: -1.31 (0.21), residues: 596 loop : -0.39 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 531 HIS 0.004 0.001 HIS H 90 PHE 0.029 0.002 PHE G 32 TYR 0.018 0.002 TYR H 86 ARG 0.006 0.001 ARG E 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8899 (t80) cc_final: 0.8646 (t80) REVERT: B 603 ILE cc_start: 0.8596 (tt) cc_final: 0.6449 (tt) REVERT: C 59 TYR cc_start: 0.9469 (p90) cc_final: 0.9104 (p90) REVERT: E 51 LEU cc_start: 0.6517 (mt) cc_final: 0.6060 (mt) REVERT: F 595 GLN cc_start: 0.9384 (tm-30) cc_final: 0.8836 (tm-30) REVERT: G 34 MET cc_start: 0.9168 (mmm) cc_final: 0.6845 (tpp) REVERT: G 36 TRP cc_start: 0.8969 (m100) cc_final: 0.8636 (m100) REVERT: G 90 TYR cc_start: 0.9071 (m-10) cc_final: 0.8429 (m-80) REVERT: H 38 GLN cc_start: 0.9058 (pm20) cc_final: 0.8834 (pm20) REVERT: H 73 LEU cc_start: 0.9234 (tp) cc_final: 0.8954 (tp) REVERT: H 96 PHE cc_start: 0.8731 (m-10) cc_final: 0.8426 (m-10) REVERT: I 85 ASP cc_start: 0.9493 (m-30) cc_final: 0.9127 (t70) REVERT: J 37 PHE cc_start: 0.8518 (p90) cc_final: 0.7837 (p90) REVERT: J 53 TRP cc_start: 0.8650 (t-100) cc_final: 0.7983 (t-100) REVERT: J 100 MET cc_start: 0.9185 (ttt) cc_final: 0.8911 (mtt) REVERT: J 102 TYR cc_start: 0.8800 (t80) cc_final: 0.8257 (t80) REVERT: N 90 TYR cc_start: 0.8882 (m-10) cc_final: 0.8460 (m-10) REVERT: N 109 VAL cc_start: 0.9380 (t) cc_final: 0.8796 (t) REVERT: P 73 LEU cc_start: 0.9556 (tt) cc_final: 0.9302 (tt) REVERT: Q 53 TRP cc_start: 0.7057 (m100) cc_final: 0.6704 (m100) REVERT: Q 100 MET cc_start: 0.8786 (ttt) cc_final: 0.8469 (ttt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3071 time to fit residues: 75.4096 Evaluate side-chains 115 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 0.0470 chunk 167 optimal weight: 8.9990 chunk 174 optimal weight: 0.0370 chunk 184 optimal weight: 3.9990 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17302 Z= 0.186 Angle : 0.647 14.019 23483 Z= 0.340 Chirality : 0.043 0.272 2635 Planarity : 0.004 0.049 2987 Dihedral : 7.667 76.854 2807 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.51 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 2105 helix: -0.72 (0.38), residues: 176 sheet: -1.22 (0.19), residues: 662 loop : -0.42 (0.19), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.003 0.001 HIS H 90 PHE 0.028 0.002 PHE G 32 TYR 0.015 0.002 TYR I 49 ARG 0.005 0.000 ARG E 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8908 (t80) cc_final: 0.8638 (t80) REVERT: B 578 GLU cc_start: 0.9107 (pt0) cc_final: 0.8741 (pt0) REVERT: B 603 ILE cc_start: 0.8575 (tt) cc_final: 0.6342 (tt) REVERT: C 59 TYR cc_start: 0.9462 (p90) cc_final: 0.9093 (p90) REVERT: C 102 TYR cc_start: 0.8833 (p90) cc_final: 0.8614 (p90) REVERT: D 87 PHE cc_start: 0.9395 (m-80) cc_final: 0.9185 (m-10) REVERT: F 595 GLN cc_start: 0.9345 (tm-30) cc_final: 0.8904 (tm-30) REVERT: G 34 MET cc_start: 0.9109 (mmm) cc_final: 0.7042 (tpp) REVERT: G 36 TRP cc_start: 0.9001 (m100) cc_final: 0.8521 (m100) REVERT: H 73 LEU cc_start: 0.9238 (tp) cc_final: 0.8962 (tp) REVERT: H 96 PHE cc_start: 0.9050 (m-10) cc_final: 0.8767 (m-10) REVERT: I 85 ASP cc_start: 0.9478 (m-30) cc_final: 0.9082 (t70) REVERT: J 27 PHE cc_start: 0.8323 (t80) cc_final: 0.8122 (t80) REVERT: J 37 PHE cc_start: 0.8468 (p90) cc_final: 0.7790 (p90) REVERT: J 53 TRP cc_start: 0.8649 (t-100) cc_final: 0.7969 (t-100) REVERT: J 100 MET cc_start: 0.9134 (ttt) cc_final: 0.8878 (mtt) REVERT: J 102 TYR cc_start: 0.8808 (t80) cc_final: 0.8493 (t80) REVERT: K 132 PHE cc_start: 0.6401 (t80) cc_final: 0.6129 (t80) REVERT: N 90 TYR cc_start: 0.8889 (m-10) cc_final: 0.8520 (m-10) REVERT: N 109 VAL cc_start: 0.9383 (t) cc_final: 0.9101 (t) REVERT: P 4 MET cc_start: 0.7751 (pmm) cc_final: 0.7466 (pmm) REVERT: P 73 LEU cc_start: 0.9571 (tt) cc_final: 0.9317 (tt) REVERT: Q 53 TRP cc_start: 0.7130 (m100) cc_final: 0.6436 (m100) REVERT: Q 100 MET cc_start: 0.8766 (ttt) cc_final: 0.8442 (ttt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3117 time to fit residues: 79.2771 Evaluate side-chains 120 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 17302 Z= 0.426 Angle : 0.870 11.667 23483 Z= 0.460 Chirality : 0.048 0.243 2635 Planarity : 0.006 0.056 2987 Dihedral : 8.355 86.828 2807 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 46.65 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.36 % Favored : 90.02 % Rotamer: Outliers : 0.06 % Allowed : 0.22 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.18), residues: 2105 helix: -1.71 (0.33), residues: 188 sheet: -1.48 (0.18), residues: 701 loop : -0.90 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP G 36 HIS 0.011 0.002 HIS B 602 PHE 0.049 0.003 PHE K 248 TYR 0.031 0.003 TYR H 86 ARG 0.011 0.001 ARG E 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.9048 (t80) cc_final: 0.8671 (t80) REVERT: B 578 GLU cc_start: 0.9161 (pt0) cc_final: 0.8783 (pt0) REVERT: C 59 TYR cc_start: 0.9486 (p90) cc_final: 0.9065 (p90) REVERT: C 102 TYR cc_start: 0.8894 (p90) cc_final: 0.8654 (p90) REVERT: E 51 LEU cc_start: 0.6875 (mt) cc_final: 0.6634 (mt) REVERT: F 595 GLN cc_start: 0.9379 (tm-30) cc_final: 0.8971 (tm-30) REVERT: F 603 ILE cc_start: 0.8140 (pt) cc_final: 0.6946 (pt) REVERT: F 604 LEU cc_start: 0.8156 (mp) cc_final: 0.7472 (mp) REVERT: G 34 MET cc_start: 0.9052 (mmm) cc_final: 0.7638 (mmm) REVERT: G 36 TRP cc_start: 0.9011 (m100) cc_final: 0.8704 (m100) REVERT: G 80 MET cc_start: 0.9223 (pmm) cc_final: 0.9016 (pmm) REVERT: H 38 GLN cc_start: 0.9162 (pm20) cc_final: 0.8961 (pm20) REVERT: J 37 PHE cc_start: 0.8656 (p90) cc_final: 0.7307 (p90) REVERT: J 102 TYR cc_start: 0.8830 (t80) cc_final: 0.8407 (t80) REVERT: P 4 MET cc_start: 0.8040 (pmm) cc_final: 0.7577 (pmm) REVERT: P 73 LEU cc_start: 0.9614 (tt) cc_final: 0.9381 (tt) REVERT: Q 100 MET cc_start: 0.8877 (ttt) cc_final: 0.8622 (ttt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2949 time to fit residues: 66.3247 Evaluate side-chains 109 residues out of total 1805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.040991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.033328 restraints weight = 238728.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.034205 restraints weight = 149790.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.034817 restraints weight = 106675.987| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17302 Z= 0.298 Angle : 0.742 10.086 23483 Z= 0.393 Chirality : 0.045 0.257 2635 Planarity : 0.005 0.046 2987 Dihedral : 8.157 89.690 2807 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 38.58 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.55 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.84 (0.18), residues: 2105 helix: -1.52 (0.34), residues: 191 sheet: -1.54 (0.18), residues: 711 loop : -0.87 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP G 36 HIS 0.006 0.001 HIS O 91 PHE 0.029 0.003 PHE G 32 TYR 0.029 0.002 TYR H 86 ARG 0.009 0.001 ARG E 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.26 seconds wall clock time: 58 minutes 3.89 seconds (3483.89 seconds total)