Starting phenix.real_space_refine on Fri Feb 16 11:44:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejh_28182/02_2024/8ejh_28182.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejh_28182/02_2024/8ejh_28182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejh_28182/02_2024/8ejh_28182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejh_28182/02_2024/8ejh_28182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejh_28182/02_2024/8ejh_28182.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejh_28182/02_2024/8ejh_28182.pdb" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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 105 5.16 5 C 9492 2.51 5 N 2418 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15186 Number of models: 1 Model: "" Number of chains: 45 Chain: "C" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "c" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "A" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "b" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "a" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "h" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "l" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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: "Q" 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "W" 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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: "Z" 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.89, per 1000 atoms: 0.52 Number of scatterers: 15186 At special positions: 0 Unit cell: (135.7, 148.35, 121.9, 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 105 16.00 O 3171 8.00 N 2418 7.00 C 9492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.04 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.02 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.02 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.02 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.08 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.06 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " distance=2.08 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 104 " distance=2.06 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 104 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN V 4 " - " MAN V 5 " " MAN i 4 " - " MAN i 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA E 3 " - " MAN J 201 " " MAN E 4 " - " MAN E 5 " " BMA P 3 " - " MAN h 201 " " MAN P 4 " - " MAN P 5 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " " BMA Y 3 " - " MAN H 201 " " MAN Y 4 " - " MAN Y 5 " " BMA i 3 " - " MAN i 4 " " MAN i 6 " - " MAN i 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 6 " " BMA Y 3 " - " MAN Y 4 " " BMA i 3 " - " MAN i 6 " " BMA k 3 " - " MAN k 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG D 1 " - " ASN C 79 " " NAG E 1 " - " ASN C 89 " " NAG F 1 " - " ASN C 99 " " NAG G 1 " - " ASN C 109 " " NAG I 1 " - " ASN C 119 " " NAG M 1 " - " ASN C 167 " " NAG N 1 " - " ASN C 224 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 89 " " NAG Q 1 " - " ASN B 99 " " NAG R 1 " - " ASN B 109 " " NAG S 1 " - " ASN B 119 " " NAG T 1 " - " ASN B 167 " " NAG U 1 " - " ASN B 224 " " NAG V 1 " - " ASN c 365 " " NAG W 1 " - " ASN c 373 " " NAG X 1 " - " ASN A 79 " " NAG Y 1 " - " ASN A 89 " " NAG Z 1 " - " ASN A 99 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " " NAG d 1 " - " ASN A 109 " " NAG e 1 " - " ASN A 119 " " NAG f 1 " - " ASN A 167 " " NAG g 1 " - " ASN A 224 " " NAG i 1 " - " ASN b 365 " " NAG j 1 " - " ASN b 373 " " NAG k 1 " - " ASN a 365 " " NAG m 1 " - " ASN a 373 " Time building additional restraints: 6.58 Conformation dependent library (CDL) restraints added in 2.3 seconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3270 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 30 sheets defined 26.9% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.292A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.293A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'c' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 302 through 304 No H-bonds generated for 'chain 'c' and resid 302 through 304' Processing helix chain 'c' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU c 326 " --> pdb=" O ALA c 322 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 339 Processing helix chain 'c' and resid 340 through 345 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.969A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 424 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 76 through 81 removed outlier: 4.292A pdb=" N MET A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'b' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS b 301 " --> pdb=" O ALA b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 302 through 304 No H-bonds generated for 'chain 'b' and resid 302 through 304' Processing helix chain 'b' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU b 326 " --> pdb=" O ALA b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 339 Processing helix chain 'b' and resid 340 through 345 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.969A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 424 Processing helix chain 'a' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 302 through 304 No H-bonds generated for 'chain 'a' and resid 302 through 304' Processing helix chain 'a' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU a 326 " --> pdb=" O ALA a 322 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 339 Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.969A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 424 Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'J' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE J 37 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 72 Processing helix chain 'J' and resid 82 through 84 No H-bonds generated for 'chain 'J' and resid 82 through 84' Processing helix chain 'K' and resid 95 through 99 Processing helix chain 'h' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE h 37 " --> pdb=" O PHE h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 72 Processing helix chain 'h' and resid 82 through 84 No H-bonds generated for 'chain 'h' and resid 82 through 84' Processing helix chain 'l' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 72 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 88 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 88 Processing sheet with id=AA5, first strand: chain 'c' and resid 279 through 280 Processing sheet with id=AA6, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 66 through 72 Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 88 Processing sheet with id=AA9, first strand: chain 'b' and resid 279 through 280 Processing sheet with id=AB1, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'a' and resid 279 through 280 Processing sheet with id=AB3, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER H 79 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS H 104 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP H 118 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG H 106 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'J' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER J 79 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS J 104 " --> pdb=" O TRP J 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP J 118 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG J 106 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN K 43 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU K 52 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'h' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER h 79 " --> pdb=" O SER h 88 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS h 104 " --> pdb=" O TRP h 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP h 118 " --> pdb=" O CYS h 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG h 106 " --> pdb=" O ASP h 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'l' and resid 4 through 5 Processing sheet with id=AD2, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN l 43 " --> pdb=" O LEU l 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU l 52 " --> pdb=" O GLN l 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 10 through 12 606 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2736 1.32 - 1.46: 5318 1.46 - 1.59: 7267 1.59 - 1.73: 42 1.73 - 1.87: 153 Bond restraints: 15516 Sorted by residual: bond pdb=" CB HIS K 44 " pdb=" CG HIS K 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.41e+01 bond pdb=" CB HIS L 44 " pdb=" CG HIS L 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.40e+01 bond pdb=" CB HIS l 44 " pdb=" CG HIS l 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.39e+01 bond pdb=" CB HIS L 106 " pdb=" CG HIS L 106 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.06e+01 bond pdb=" CB HIS l 106 " pdb=" CG HIS l 106 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 ... (remaining 15511 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.29: 558 106.29 - 113.28: 8324 113.28 - 120.27: 6393 120.27 - 127.26: 5554 127.26 - 134.25: 210 Bond angle restraints: 21039 Sorted by residual: angle pdb=" N ASP c 311 " pdb=" CA ASP c 311 " pdb=" C ASP c 311 " ideal model delta sigma weight residual 111.69 101.98 9.71 1.23e+00 6.61e-01 6.24e+01 angle pdb=" N ASP a 311 " pdb=" CA ASP a 311 " pdb=" C ASP a 311 " ideal model delta sigma weight residual 111.69 102.01 9.68 1.23e+00 6.61e-01 6.20e+01 angle pdb=" N ASP b 311 " pdb=" CA ASP b 311 " pdb=" C ASP b 311 " ideal model delta sigma weight residual 111.69 102.01 9.68 1.23e+00 6.61e-01 6.19e+01 angle pdb=" C GLN h 44 " pdb=" N PRO h 45 " pdb=" CA PRO h 45 " ideal model delta sigma weight residual 119.66 124.99 -5.33 7.30e-01 1.88e+00 5.32e+01 angle pdb=" C GLN J 44 " pdb=" N PRO J 45 " pdb=" CA PRO J 45 " ideal model delta sigma weight residual 119.66 124.98 -5.32 7.30e-01 1.88e+00 5.30e+01 ... (remaining 21034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 9943 21.81 - 43.62: 275 43.62 - 65.43: 51 65.43 - 87.24: 111 87.24 - 109.05: 78 Dihedral angle restraints: 10458 sinusoidal: 5352 harmonic: 5106 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 104 " pdb=" CB CYS K 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.20 -62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS l 23 " pdb=" SG CYS l 23 " pdb=" SG CYS l 104 " pdb=" CB CYS l 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.20 -62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.19 -62.19 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 10455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1641 0.101 - 0.202: 564 0.202 - 0.302: 236 0.302 - 0.403: 103 0.403 - 0.504: 60 Chirality restraints: 2604 Sorted by residual: chirality pdb=" C1 MAN V 6 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.89e+02 chirality pdb=" C1 MAN i 6 " pdb=" O6 BMA i 3 " pdb=" C2 MAN i 6 " pdb=" O5 MAN i 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.87e+02 chirality pdb=" C1 MAN k 6 " pdb=" O6 BMA k 3 " pdb=" C2 MAN k 6 " pdb=" O5 MAN k 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.86e+02 ... (remaining 2601 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG Y 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG P 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG E 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.030 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4647 2.84 - 3.35: 13654 3.35 - 3.87: 25437 3.87 - 4.38: 29641 4.38 - 4.90: 47957 Nonbonded interactions: 121336 Sorted by model distance: nonbonded pdb=" O4 MAN P 4 " pdb=" O6 MAN P 4 " model vdw 2.321 2.440 nonbonded pdb=" O4 MAN E 4 " pdb=" O6 MAN E 4 " model vdw 2.321 2.440 nonbonded pdb=" O4 MAN Y 4 " pdb=" O6 MAN Y 4 " model vdw 2.321 2.440 nonbonded pdb=" O4 MAN k 4 " pdb=" O6 MAN k 4 " model vdw 2.380 2.440 nonbonded pdb=" O4 MAN i 4 " pdb=" O6 MAN i 4 " model vdw 2.380 2.440 ... (remaining 121331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'd' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'Q' selection = chain 'S' selection = chain 'W' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'm' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'h' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'V' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.410 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.900 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.270 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.021 0.117 15516 Z= 1.360 Angle : 1.825 10.041 21039 Z= 1.158 Chirality : 0.146 0.504 2604 Planarity : 0.011 0.193 2514 Dihedral : 17.279 109.053 7107 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1731 helix: -0.37 (0.25), residues: 372 sheet: 0.26 (0.26), residues: 375 loop : -0.05 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.010 TRP H 52 HIS 0.006 0.002 HIS H 113 PHE 0.027 0.006 PHE l 99 TYR 0.048 0.007 TYR B 253 ARG 0.006 0.001 ARG h 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 1.674 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: C 80 MET cc_start: 0.8364 (mmm) cc_final: 0.7641 (mmm) REVERT: C 194 MET cc_start: 0.8339 (tpp) cc_final: 0.7889 (tpp) REVERT: B 80 MET cc_start: 0.8297 (mmm) cc_final: 0.7502 (mmt) REVERT: B 194 MET cc_start: 0.8366 (tpp) cc_final: 0.8142 (tpp) REVERT: A 80 MET cc_start: 0.8351 (mmm) cc_final: 0.7756 (mmt) REVERT: A 194 MET cc_start: 0.8278 (tpp) cc_final: 0.7908 (ttm) REVERT: H 13 LEU cc_start: 0.8014 (mt) cc_final: 0.7703 (pp) REVERT: H 52 TRP cc_start: 0.8554 (t60) cc_final: 0.8283 (t60) REVERT: H 56 ILE cc_start: 0.9329 (tt) cc_final: 0.9052 (tt) REVERT: H 68 ASN cc_start: 0.8838 (t0) cc_final: 0.8400 (t0) REVERT: H 80 VAL cc_start: 0.8784 (p) cc_final: 0.8571 (t) REVERT: H 98 ASP cc_start: 0.8127 (m-30) cc_final: 0.7786 (m-30) REVERT: L 3 THR cc_start: 0.9317 (p) cc_final: 0.8990 (p) REVERT: L 5 THR cc_start: 0.8172 (m) cc_final: 0.7895 (p) REVERT: L 18 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7703 (ttp80) REVERT: L 90 THR cc_start: 0.8425 (m) cc_final: 0.8116 (p) REVERT: L 99 PHE cc_start: 0.6940 (m-80) cc_final: 0.6722 (m-80) REVERT: J 52 TRP cc_start: 0.8638 (t60) cc_final: 0.8388 (t60) REVERT: J 87 PHE cc_start: 0.8165 (p90) cc_final: 0.7902 (p90) REVERT: J 98 ASP cc_start: 0.7786 (m-30) cc_final: 0.7563 (m-30) REVERT: J 122 THR cc_start: 0.7888 (m) cc_final: 0.7672 (p) REVERT: K 5 THR cc_start: 0.8308 (m) cc_final: 0.8083 (p) REVERT: K 90 THR cc_start: 0.8444 (m) cc_final: 0.8235 (p) REVERT: K 99 PHE cc_start: 0.6802 (m-80) cc_final: 0.6418 (m-80) REVERT: h 13 LEU cc_start: 0.7856 (mt) cc_final: 0.7511 (pp) REVERT: h 87 PHE cc_start: 0.8310 (p90) cc_final: 0.8094 (p90) REVERT: l 18 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7700 (ttp80) REVERT: l 90 THR cc_start: 0.8466 (m) cc_final: 0.8188 (p) REVERT: l 99 PHE cc_start: 0.6714 (m-80) cc_final: 0.6325 (m-80) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.3140 time to fit residues: 234.6833 Evaluate side-chains 284 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 0.2980 chunk 44 optimal weight: 0.0050 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN c 302 ASN b 302 ASN a 302 ASN a 416 GLN L 105 GLN J 68 ASN K 6 GLN K 105 GLN h 68 ASN l 6 GLN l 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15516 Z= 0.264 Angle : 0.810 8.717 21039 Z= 0.408 Chirality : 0.048 0.288 2604 Planarity : 0.005 0.033 2514 Dihedral : 14.420 74.544 3903 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.01 % Allowed : 10.59 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1731 helix: 0.53 (0.28), residues: 378 sheet: 0.28 (0.25), residues: 405 loop : -0.34 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP h 52 HIS 0.010 0.002 HIS a 305 PHE 0.021 0.002 PHE H 30 TYR 0.025 0.002 TYR a 419 ARG 0.007 0.001 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 360 time to evaluate : 1.848 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: C 194 MET cc_start: 0.8601 (tpp) cc_final: 0.8312 (tpp) REVERT: B 82 MET cc_start: 0.8778 (ptp) cc_final: 0.8576 (ptp) REVERT: B 125 LYS cc_start: 0.8881 (tppt) cc_final: 0.8675 (tppt) REVERT: B 194 MET cc_start: 0.8642 (tpp) cc_final: 0.8266 (tpp) REVERT: c 303 GLU cc_start: 0.5972 (tp30) cc_final: 0.5721 (tp30) REVERT: c 419 TYR cc_start: 0.7460 (t80) cc_final: 0.7176 (t80) REVERT: c 420 MET cc_start: 0.7466 (mmt) cc_final: 0.6381 (tpt) REVERT: A 194 MET cc_start: 0.8624 (tpp) cc_final: 0.8337 (tpp) REVERT: b 306 ASP cc_start: 0.7994 (p0) cc_final: 0.7762 (p0) REVERT: b 414 MET cc_start: 0.8148 (tpp) cc_final: 0.7920 (tpp) REVERT: b 420 MET cc_start: 0.7517 (mmt) cc_final: 0.6938 (tpt) REVERT: a 306 ASP cc_start: 0.8014 (p0) cc_final: 0.7631 (p0) REVERT: a 409 ASN cc_start: 0.8611 (m-40) cc_final: 0.8328 (m110) REVERT: a 420 MET cc_start: 0.7651 (mmt) cc_final: 0.7023 (tpt) REVERT: H 13 LEU cc_start: 0.7941 (mt) cc_final: 0.7579 (pp) REVERT: H 98 ASP cc_start: 0.8090 (m-30) cc_final: 0.7847 (m-30) REVERT: H 118 TRP cc_start: 0.7716 (m100) cc_final: 0.7407 (m100) REVERT: L 17 GLU cc_start: 0.7978 (mp0) cc_final: 0.7655 (mp0) REVERT: L 18 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7773 (ttp80) REVERT: L 90 THR cc_start: 0.8547 (m) cc_final: 0.8272 (p) REVERT: L 94 LEU cc_start: 0.7741 (tp) cc_final: 0.7505 (tt) REVERT: L 99 PHE cc_start: 0.7246 (m-80) cc_final: 0.6684 (m-80) REVERT: L 128 LYS cc_start: 0.7966 (tmmt) cc_final: 0.7735 (pttm) REVERT: J 5 GLN cc_start: 0.7080 (tp40) cc_final: 0.6732 (tp-100) REVERT: J 52 TRP cc_start: 0.8388 (t60) cc_final: 0.7804 (t60) REVERT: K 18 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7752 (ttp80) REVERT: K 99 PHE cc_start: 0.7211 (m-80) cc_final: 0.6901 (m-80) REVERT: h 43 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8592 (mtm110) REVERT: h 53 ILE cc_start: 0.8930 (mt) cc_final: 0.8671 (mt) REVERT: h 87 PHE cc_start: 0.8505 (p90) cc_final: 0.8269 (p90) REVERT: l 17 GLU cc_start: 0.8223 (mp0) cc_final: 0.7897 (mp0) REVERT: l 18 ARG cc_start: 0.8397 (ttm170) cc_final: 0.7677 (ttp80) REVERT: l 90 THR cc_start: 0.8431 (m) cc_final: 0.8150 (p) REVERT: l 122 THR cc_start: 0.8306 (p) cc_final: 0.7981 (p) outliers start: 31 outliers final: 22 residues processed: 376 average time/residue: 0.2927 time to fit residues: 156.6842 Evaluate side-chains 296 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 274 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 273 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 327 LYS Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 0.0470 chunk 129 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 HIS B 170 HIS c 423 GLN A 170 HIS l 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15516 Z= 0.208 Angle : 0.729 12.061 21039 Z= 0.357 Chirality : 0.047 0.256 2604 Planarity : 0.004 0.036 2514 Dihedral : 10.433 61.886 3903 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.38 % Allowed : 11.83 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1731 helix: 0.79 (0.28), residues: 375 sheet: 0.38 (0.25), residues: 426 loop : -0.66 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 52 HIS 0.008 0.001 HIS B 230 PHE 0.033 0.002 PHE J 87 TYR 0.030 0.002 TYR a 419 ARG 0.006 0.001 ARG c 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 301 time to evaluate : 1.583 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: C 125 LYS cc_start: 0.8659 (tppt) cc_final: 0.8341 (tppt) REVERT: B 151 GLU cc_start: 0.8069 (pm20) cc_final: 0.7818 (pm20) REVERT: c 303 GLU cc_start: 0.6093 (tp30) cc_final: 0.5724 (tp30) REVERT: c 419 TYR cc_start: 0.7477 (t80) cc_final: 0.7217 (t80) REVERT: c 420 MET cc_start: 0.7618 (mmt) cc_final: 0.6617 (tpt) REVERT: A 80 MET cc_start: 0.8156 (tpp) cc_final: 0.7591 (mmt) REVERT: A 245 LEU cc_start: 0.8170 (tp) cc_final: 0.7856 (tp) REVERT: b 306 ASP cc_start: 0.8041 (p0) cc_final: 0.7587 (p0) REVERT: b 418 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8187 (mt-10) REVERT: b 420 MET cc_start: 0.7759 (mmt) cc_final: 0.6997 (tpt) REVERT: a 306 ASP cc_start: 0.8036 (p0) cc_final: 0.7642 (p0) REVERT: a 409 ASN cc_start: 0.8456 (m-40) cc_final: 0.8198 (m110) REVERT: a 420 MET cc_start: 0.8021 (mmt) cc_final: 0.7460 (tpt) REVERT: H 98 ASP cc_start: 0.8136 (m-30) cc_final: 0.7863 (m-30) REVERT: H 112 TYR cc_start: 0.8144 (p90) cc_final: 0.7798 (p90) REVERT: H 118 TRP cc_start: 0.7659 (m100) cc_final: 0.7428 (m100) REVERT: L 17 GLU cc_start: 0.8157 (mp0) cc_final: 0.7955 (mp0) REVERT: L 18 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7764 (ttp80) REVERT: L 94 LEU cc_start: 0.7776 (tp) cc_final: 0.7481 (tt) REVERT: L 99 PHE cc_start: 0.7245 (m-80) cc_final: 0.6746 (m-80) REVERT: L 122 THR cc_start: 0.7837 (p) cc_final: 0.7572 (p) REVERT: J 5 GLN cc_start: 0.7249 (tp40) cc_final: 0.6934 (tp-100) REVERT: K 1 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: K 17 GLU cc_start: 0.8190 (mp0) cc_final: 0.7947 (mp0) REVERT: K 99 PHE cc_start: 0.7397 (m-80) cc_final: 0.7027 (m-80) REVERT: h 53 ILE cc_start: 0.8948 (mt) cc_final: 0.8717 (mt) REVERT: h 87 PHE cc_start: 0.8467 (p90) cc_final: 0.8232 (p90) REVERT: l 99 PHE cc_start: 0.7181 (m-80) cc_final: 0.6725 (m-80) REVERT: l 122 THR cc_start: 0.8227 (p) cc_final: 0.7861 (p) outliers start: 52 outliers final: 31 residues processed: 326 average time/residue: 0.2830 time to fit residues: 132.7377 Evaluate side-chains 290 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 258 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 326 LEU Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 165 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 149 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN A 149 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15516 Z= 0.211 Angle : 0.679 11.495 21039 Z= 0.330 Chirality : 0.044 0.253 2604 Planarity : 0.004 0.037 2514 Dihedral : 8.201 53.864 3903 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.31 % Allowed : 13.45 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1731 helix: 1.07 (0.28), residues: 372 sheet: 0.39 (0.25), residues: 429 loop : -0.71 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP H 52 HIS 0.008 0.001 HIS c 305 PHE 0.012 0.001 PHE H 30 TYR 0.026 0.001 TYR a 419 ARG 0.004 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 286 time to evaluate : 1.698 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: C 194 MET cc_start: 0.8254 (tpp) cc_final: 0.7924 (ttp) REVERT: c 419 TYR cc_start: 0.7370 (t80) cc_final: 0.7118 (t80) REVERT: c 420 MET cc_start: 0.7725 (mmt) cc_final: 0.6778 (tpt) REVERT: A 194 MET cc_start: 0.8348 (tpt) cc_final: 0.8013 (tpp) REVERT: A 245 LEU cc_start: 0.8240 (tp) cc_final: 0.7949 (tp) REVERT: b 306 ASP cc_start: 0.8083 (p0) cc_final: 0.7872 (p0) REVERT: b 418 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8278 (mt-10) REVERT: b 420 MET cc_start: 0.7843 (mmt) cc_final: 0.7135 (tpt) REVERT: a 420 MET cc_start: 0.8082 (mmt) cc_final: 0.7459 (tpt) REVERT: H 112 TYR cc_start: 0.8147 (p90) cc_final: 0.7732 (p90) REVERT: H 118 TRP cc_start: 0.7838 (m100) cc_final: 0.7476 (m100) REVERT: L 18 ARG cc_start: 0.8278 (ttm170) cc_final: 0.7725 (ttp80) REVERT: L 94 LEU cc_start: 0.7833 (tp) cc_final: 0.7476 (tt) REVERT: L 99 PHE cc_start: 0.7375 (m-80) cc_final: 0.6891 (m-80) REVERT: J 5 GLN cc_start: 0.7297 (tp40) cc_final: 0.6975 (tp-100) REVERT: J 52 TRP cc_start: 0.8424 (t60) cc_final: 0.8157 (t60) REVERT: K 17 GLU cc_start: 0.8248 (mp0) cc_final: 0.7455 (mp0) REVERT: K 99 PHE cc_start: 0.7361 (m-80) cc_final: 0.7024 (m-80) REVERT: h 87 PHE cc_start: 0.8530 (p90) cc_final: 0.8274 (p90) REVERT: l 122 THR cc_start: 0.8154 (p) cc_final: 0.7893 (p) outliers start: 51 outliers final: 35 residues processed: 315 average time/residue: 0.2783 time to fit residues: 127.2175 Evaluate side-chains 282 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 247 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 287 GLU Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 ASN ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS L 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15516 Z= 0.369 Angle : 0.768 10.690 21039 Z= 0.375 Chirality : 0.046 0.260 2604 Planarity : 0.004 0.039 2514 Dihedral : 7.643 47.485 3903 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.77 % Allowed : 13.45 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1731 helix: 1.07 (0.28), residues: 375 sheet: 0.23 (0.26), residues: 408 loop : -0.90 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP H 52 HIS 0.009 0.002 HIS L 44 PHE 0.020 0.002 PHE K 76 TYR 0.030 0.002 TYR a 419 ARG 0.004 0.001 ARG L 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 264 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.8400 (tpp) cc_final: 0.8013 (ttp) REVERT: c 311 ASP cc_start: 0.7890 (t0) cc_final: 0.7626 (t0) REVERT: c 419 TYR cc_start: 0.7423 (t80) cc_final: 0.7179 (t80) REVERT: c 420 MET cc_start: 0.7605 (mmt) cc_final: 0.6689 (tpt) REVERT: A 67 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7126 (tt0) REVERT: b 306 ASP cc_start: 0.8049 (p0) cc_final: 0.7798 (p0) REVERT: b 311 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7927 (t0) REVERT: b 414 MET cc_start: 0.7936 (tpt) cc_final: 0.7694 (tpp) REVERT: b 418 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8530 (mm-30) REVERT: b 420 MET cc_start: 0.7728 (mmt) cc_final: 0.7172 (tpt) REVERT: a 306 ASP cc_start: 0.7504 (p0) cc_final: 0.7234 (p0) REVERT: a 311 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.6972 (t0) REVERT: a 348 GLN cc_start: 0.6100 (mt0) cc_final: 0.5151 (tt0) REVERT: a 410 MET cc_start: 0.8475 (mtp) cc_final: 0.8066 (ttm) REVERT: a 420 MET cc_start: 0.8075 (mmt) cc_final: 0.7496 (tpt) REVERT: H 112 TYR cc_start: 0.8291 (p90) cc_final: 0.7915 (p90) REVERT: L 18 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7640 (ttp80) REVERT: L 94 LEU cc_start: 0.7925 (tp) cc_final: 0.7541 (tt) REVERT: L 99 PHE cc_start: 0.7308 (m-80) cc_final: 0.6932 (m-80) REVERT: J 5 GLN cc_start: 0.7282 (tp40) cc_final: 0.7015 (tp-100) REVERT: J 52 TRP cc_start: 0.8516 (t60) cc_final: 0.8137 (t60) REVERT: K 17 GLU cc_start: 0.8326 (mp0) cc_final: 0.7504 (mp0) REVERT: K 99 PHE cc_start: 0.7427 (m-80) cc_final: 0.7079 (m-80) REVERT: K 122 THR cc_start: 0.8485 (p) cc_final: 0.8234 (p) REVERT: K 125 GLU cc_start: 0.5934 (tt0) cc_final: 0.5530 (tt0) REVERT: h 4 LEU cc_start: 0.8235 (tt) cc_final: 0.8008 (mt) REVERT: h 13 LEU cc_start: 0.7785 (mt) cc_final: 0.7412 (pp) REVERT: l 99 PHE cc_start: 0.7268 (m-80) cc_final: 0.6827 (m-80) REVERT: l 122 THR cc_start: 0.8352 (p) cc_final: 0.8097 (p) outliers start: 58 outliers final: 40 residues processed: 301 average time/residue: 0.2721 time to fit residues: 119.5002 Evaluate side-chains 284 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 242 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 287 GLU Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 165 optimal weight: 0.3980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15516 Z= 0.214 Angle : 0.674 10.069 21039 Z= 0.330 Chirality : 0.043 0.260 2604 Planarity : 0.004 0.045 2514 Dihedral : 7.080 49.707 3903 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.64 % Allowed : 14.75 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1731 helix: 1.21 (0.29), residues: 372 sheet: 0.13 (0.25), residues: 426 loop : -0.83 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP H 52 HIS 0.004 0.001 HIS A 141 PHE 0.022 0.002 PHE h 87 TYR 0.026 0.001 TYR a 419 ARG 0.005 0.000 ARG b 422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 260 time to evaluate : 1.797 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: C 194 MET cc_start: 0.8301 (tpp) cc_final: 0.7933 (ttp) REVERT: B 125 LYS cc_start: 0.9117 (tmtt) cc_final: 0.8883 (tppt) REVERT: c 303 GLU cc_start: 0.5988 (tp30) cc_final: 0.5670 (tp30) REVERT: c 311 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7357 (t0) REVERT: c 348 GLN cc_start: 0.5834 (mt0) cc_final: 0.5173 (tt0) REVERT: c 419 TYR cc_start: 0.7356 (t80) cc_final: 0.7105 (t80) REVERT: c 420 MET cc_start: 0.7621 (mmt) cc_final: 0.6700 (tpt) REVERT: A 67 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7266 (tt0) REVERT: b 306 ASP cc_start: 0.7973 (p0) cc_final: 0.7741 (p0) REVERT: b 311 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7900 (t70) REVERT: b 420 MET cc_start: 0.7871 (mmt) cc_final: 0.7171 (tpt) REVERT: a 306 ASP cc_start: 0.7575 (p0) cc_final: 0.7325 (p0) REVERT: a 311 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7543 (t0) REVERT: a 348 GLN cc_start: 0.5883 (mt0) cc_final: 0.4993 (tt0) REVERT: a 410 MET cc_start: 0.8470 (mtp) cc_final: 0.8052 (ttm) REVERT: a 420 MET cc_start: 0.8101 (mmt) cc_final: 0.7505 (tpt) REVERT: H 112 TYR cc_start: 0.8185 (p90) cc_final: 0.7835 (p90) REVERT: L 18 ARG cc_start: 0.8406 (ttm170) cc_final: 0.7631 (ttp80) REVERT: L 94 LEU cc_start: 0.7906 (tp) cc_final: 0.7575 (tt) REVERT: L 99 PHE cc_start: 0.7223 (m-80) cc_final: 0.6820 (m-80) REVERT: J 5 GLN cc_start: 0.7145 (tp40) cc_final: 0.6940 (tp-100) REVERT: J 52 TRP cc_start: 0.8499 (t60) cc_final: 0.8106 (t60) REVERT: K 17 GLU cc_start: 0.8320 (mp0) cc_final: 0.7520 (mp0) REVERT: K 42 TYR cc_start: 0.8879 (m-80) cc_final: 0.8494 (m-80) REVERT: h 87 PHE cc_start: 0.8633 (p90) cc_final: 0.8425 (p90) outliers start: 56 outliers final: 39 residues processed: 297 average time/residue: 0.2747 time to fit residues: 119.3349 Evaluate side-chains 273 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 231 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 94 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 164 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15516 Z= 0.189 Angle : 0.652 13.504 21039 Z= 0.318 Chirality : 0.042 0.252 2604 Planarity : 0.004 0.044 2514 Dihedral : 6.648 51.787 3903 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.57 % Allowed : 15.07 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1731 helix: 1.28 (0.29), residues: 372 sheet: 0.12 (0.25), residues: 426 loop : -0.84 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 52 HIS 0.004 0.001 HIS a 305 PHE 0.023 0.001 PHE J 87 TYR 0.017 0.001 TYR b 419 ARG 0.005 0.000 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 253 time to evaluate : 1.699 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: C 194 MET cc_start: 0.8348 (tpp) cc_final: 0.7959 (ttp) REVERT: B 125 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8911 (tppt) REVERT: c 303 GLU cc_start: 0.6052 (tp30) cc_final: 0.5763 (tp30) REVERT: c 348 GLN cc_start: 0.5671 (mt0) cc_final: 0.5112 (tt0) REVERT: c 420 MET cc_start: 0.7698 (mmt) cc_final: 0.6812 (tpt) REVERT: A 67 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7317 (tt0) REVERT: b 306 ASP cc_start: 0.7993 (p0) cc_final: 0.7696 (p0) REVERT: b 311 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7906 (t70) REVERT: b 420 MET cc_start: 0.7928 (mmt) cc_final: 0.7280 (tpt) REVERT: a 306 ASP cc_start: 0.7550 (p0) cc_final: 0.7304 (p0) REVERT: a 311 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7426 (t70) REVERT: a 348 GLN cc_start: 0.5785 (mt0) cc_final: 0.4888 (tt0) REVERT: a 410 MET cc_start: 0.8534 (mtp) cc_final: 0.8089 (ttm) REVERT: a 420 MET cc_start: 0.8082 (mmt) cc_final: 0.7512 (tpt) REVERT: H 112 TYR cc_start: 0.8085 (p90) cc_final: 0.7738 (p90) REVERT: L 17 GLU cc_start: 0.8157 (mp0) cc_final: 0.7414 (mp0) REVERT: L 18 ARG cc_start: 0.8411 (ttm170) cc_final: 0.7615 (ttp80) REVERT: L 94 LEU cc_start: 0.7853 (tp) cc_final: 0.7516 (tt) REVERT: L 99 PHE cc_start: 0.7264 (m-80) cc_final: 0.6954 (m-80) REVERT: J 52 TRP cc_start: 0.8400 (t60) cc_final: 0.7983 (t60) REVERT: K 1 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: K 17 GLU cc_start: 0.8280 (mp0) cc_final: 0.7495 (mp0) REVERT: K 42 TYR cc_start: 0.8835 (m-80) cc_final: 0.8489 (m-80) REVERT: l 17 GLU cc_start: 0.8115 (mp0) cc_final: 0.7689 (mp0) outliers start: 55 outliers final: 36 residues processed: 288 average time/residue: 0.2615 time to fit residues: 111.5902 Evaluate side-chains 264 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15516 Z= 0.248 Angle : 0.682 14.192 21039 Z= 0.331 Chirality : 0.043 0.246 2604 Planarity : 0.004 0.044 2514 Dihedral : 6.714 59.736 3903 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.31 % Allowed : 15.92 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1731 helix: 1.30 (0.29), residues: 372 sheet: 0.02 (0.26), residues: 411 loop : -0.89 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 52 HIS 0.009 0.001 HIS l 44 PHE 0.046 0.002 PHE h 87 TYR 0.017 0.001 TYR b 419 ARG 0.005 0.000 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 241 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.8360 (tpp) cc_final: 0.7922 (ttp) REVERT: B 67 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7200 (tt0) REVERT: c 303 GLU cc_start: 0.6117 (tp30) cc_final: 0.5814 (tp30) REVERT: c 348 GLN cc_start: 0.5752 (mt0) cc_final: 0.5150 (tt0) REVERT: c 420 MET cc_start: 0.7724 (mmt) cc_final: 0.6909 (tpt) REVERT: b 306 ASP cc_start: 0.7970 (p0) cc_final: 0.7642 (p0) REVERT: b 311 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7942 (t70) REVERT: b 420 MET cc_start: 0.7928 (mmt) cc_final: 0.7311 (tpt) REVERT: a 306 ASP cc_start: 0.7464 (p0) cc_final: 0.7211 (p0) REVERT: a 311 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7600 (t0) REVERT: a 348 GLN cc_start: 0.5739 (mt0) cc_final: 0.4874 (tt0) REVERT: a 410 MET cc_start: 0.8578 (mtp) cc_final: 0.7982 (ttm) REVERT: a 420 MET cc_start: 0.8106 (mmt) cc_final: 0.7541 (tpt) REVERT: H 4 LEU cc_start: 0.7535 (mm) cc_final: 0.7210 (mt) REVERT: H 112 TYR cc_start: 0.8142 (p90) cc_final: 0.7772 (p90) REVERT: L 17 GLU cc_start: 0.8253 (mp0) cc_final: 0.7512 (mp0) REVERT: L 18 ARG cc_start: 0.8369 (ttm170) cc_final: 0.7583 (ttp80) REVERT: L 94 LEU cc_start: 0.7862 (tp) cc_final: 0.7538 (tt) REVERT: L 99 PHE cc_start: 0.7344 (m-80) cc_final: 0.7023 (m-80) REVERT: J 30 PHE cc_start: 0.8344 (t80) cc_final: 0.8106 (t80) REVERT: J 52 TRP cc_start: 0.8443 (t60) cc_final: 0.7992 (t60) REVERT: K 17 GLU cc_start: 0.8391 (mp0) cc_final: 0.7591 (mp0) REVERT: K 42 TYR cc_start: 0.8927 (m-80) cc_final: 0.8615 (m-80) REVERT: K 99 PHE cc_start: 0.7265 (m-80) cc_final: 0.7029 (m-80) REVERT: h 85 ASN cc_start: 0.7068 (p0) cc_final: 0.6826 (p0) REVERT: l 17 GLU cc_start: 0.8188 (mp0) cc_final: 0.7760 (mp0) outliers start: 51 outliers final: 41 residues processed: 272 average time/residue: 0.2687 time to fit residues: 107.9011 Evaluate side-chains 269 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 287 GLU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.0870 chunk 157 optimal weight: 7.9990 chunk 144 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15516 Z= 0.202 Angle : 0.678 14.232 21039 Z= 0.326 Chirality : 0.042 0.248 2604 Planarity : 0.004 0.049 2514 Dihedral : 6.472 53.104 3903 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.12 % Allowed : 16.50 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1731 helix: 1.39 (0.29), residues: 372 sheet: 0.07 (0.25), residues: 423 loop : -0.93 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP h 52 HIS 0.007 0.001 HIS a 305 PHE 0.037 0.002 PHE h 87 TYR 0.027 0.001 TYR a 419 ARG 0.012 0.000 ARG l 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 232 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.8369 (tpp) cc_final: 0.7987 (ttp) REVERT: B 67 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7200 (tt0) REVERT: c 303 GLU cc_start: 0.6077 (tp30) cc_final: 0.5793 (tp30) REVERT: c 348 GLN cc_start: 0.5664 (mt0) cc_final: 0.5158 (tt0) REVERT: c 420 MET cc_start: 0.7805 (mmt) cc_final: 0.7037 (tpt) REVERT: A 67 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7302 (tt0) REVERT: A 82 MET cc_start: 0.8750 (pmm) cc_final: 0.8364 (pmm) REVERT: A 194 MET cc_start: 0.8045 (tpp) cc_final: 0.7685 (ttm) REVERT: b 306 ASP cc_start: 0.7983 (p0) cc_final: 0.7676 (p0) REVERT: b 311 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7909 (t70) REVERT: b 410 MET cc_start: 0.8421 (mmm) cc_final: 0.8081 (mmm) REVERT: b 420 MET cc_start: 0.7930 (mmt) cc_final: 0.7299 (tpt) REVERT: a 306 ASP cc_start: 0.7465 (p0) cc_final: 0.7206 (p0) REVERT: a 311 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7558 (t0) REVERT: a 332 MET cc_start: 0.6913 (tpp) cc_final: 0.6627 (tpp) REVERT: a 348 GLN cc_start: 0.5407 (mt0) cc_final: 0.4658 (tt0) REVERT: a 410 MET cc_start: 0.8577 (mtp) cc_final: 0.8019 (ttm) REVERT: a 420 MET cc_start: 0.8156 (mmt) cc_final: 0.7642 (tpt) REVERT: L 17 GLU cc_start: 0.8303 (mp0) cc_final: 0.7626 (mp0) REVERT: L 18 ARG cc_start: 0.8392 (ttm170) cc_final: 0.7562 (ttp80) REVERT: L 86 ASP cc_start: 0.7954 (t70) cc_final: 0.7699 (t0) REVERT: L 94 LEU cc_start: 0.7841 (tp) cc_final: 0.7534 (tt) REVERT: L 99 PHE cc_start: 0.7304 (m-80) cc_final: 0.7002 (m-80) REVERT: L 127 LYS cc_start: 0.7723 (pttt) cc_final: 0.7520 (ptpt) REVERT: J 30 PHE cc_start: 0.8371 (t80) cc_final: 0.8130 (t80) REVERT: J 52 TRP cc_start: 0.8694 (t60) cc_final: 0.8279 (t60) REVERT: K 17 GLU cc_start: 0.8472 (mp0) cc_final: 0.7817 (mp0) REVERT: K 42 TYR cc_start: 0.8831 (m-80) cc_final: 0.8541 (m-80) REVERT: K 99 PHE cc_start: 0.7240 (m-80) cc_final: 0.6975 (m-80) REVERT: h 13 LEU cc_start: 0.7098 (mm) cc_final: 0.6438 (tt) REVERT: l 17 GLU cc_start: 0.8069 (mp0) cc_final: 0.7696 (mp0) outliers start: 48 outliers final: 37 residues processed: 261 average time/residue: 0.2617 time to fit residues: 101.3229 Evaluate side-chains 263 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 224 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 135 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15516 Z= 0.254 Angle : 0.702 13.624 21039 Z= 0.338 Chirality : 0.043 0.239 2604 Planarity : 0.004 0.067 2514 Dihedral : 6.478 44.047 3903 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.66 % Allowed : 17.28 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1731 helix: 1.36 (0.29), residues: 372 sheet: 0.08 (0.26), residues: 408 loop : -0.95 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP h 52 HIS 0.007 0.001 HIS a 305 PHE 0.038 0.002 PHE h 87 TYR 0.014 0.001 TYR b 419 ARG 0.013 0.001 ARG l 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 230 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.8368 (tpp) cc_final: 0.7939 (ttp) REVERT: B 67 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7218 (tt0) REVERT: B 125 LYS cc_start: 0.9165 (tmtt) cc_final: 0.8863 (tppt) REVERT: c 303 GLU cc_start: 0.6138 (tp30) cc_final: 0.5858 (tp30) REVERT: c 332 MET cc_start: 0.6365 (tpt) cc_final: 0.5694 (tpt) REVERT: c 348 GLN cc_start: 0.5811 (mt0) cc_final: 0.5121 (tt0) REVERT: c 420 MET cc_start: 0.7782 (mmt) cc_final: 0.6953 (tpt) REVERT: A 67 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7518 (tt0) REVERT: b 306 ASP cc_start: 0.7966 (p0) cc_final: 0.7631 (p0) REVERT: b 311 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7909 (t70) REVERT: b 420 MET cc_start: 0.7985 (mmt) cc_final: 0.7371 (tpt) REVERT: a 306 ASP cc_start: 0.7453 (p0) cc_final: 0.7155 (p0) REVERT: a 311 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7636 (t0) REVERT: a 332 MET cc_start: 0.7060 (tpp) cc_final: 0.6735 (tpp) REVERT: a 348 GLN cc_start: 0.5509 (mt0) cc_final: 0.5071 (tt0) REVERT: a 410 MET cc_start: 0.8579 (mtp) cc_final: 0.7945 (ttm) REVERT: a 420 MET cc_start: 0.8141 (mmt) cc_final: 0.7617 (tpt) REVERT: L 17 GLU cc_start: 0.8334 (mp0) cc_final: 0.7681 (mp0) REVERT: L 18 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7428 (ttp80) REVERT: L 86 ASP cc_start: 0.7965 (t70) cc_final: 0.7753 (t0) REVERT: L 94 LEU cc_start: 0.7757 (tp) cc_final: 0.7401 (tt) REVERT: L 99 PHE cc_start: 0.7368 (m-80) cc_final: 0.7058 (m-80) REVERT: J 30 PHE cc_start: 0.8477 (t80) cc_final: 0.8200 (t80) REVERT: J 52 TRP cc_start: 0.8784 (t60) cc_final: 0.8335 (t60) REVERT: K 17 GLU cc_start: 0.8445 (mp0) cc_final: 0.7651 (mp0) REVERT: K 42 TYR cc_start: 0.8908 (m-80) cc_final: 0.8680 (m-80) REVERT: K 99 PHE cc_start: 0.7179 (m-80) cc_final: 0.6861 (m-80) REVERT: h 13 LEU cc_start: 0.6823 (mm) cc_final: 0.6340 (tt) REVERT: l 17 GLU cc_start: 0.8104 (mp0) cc_final: 0.7734 (mp0) REVERT: l 99 PHE cc_start: 0.7182 (m-80) cc_final: 0.6962 (m-80) outliers start: 41 outliers final: 37 residues processed: 254 average time/residue: 0.2946 time to fit residues: 110.0539 Evaluate side-chains 262 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.098779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075704 restraints weight = 37920.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.078850 restraints weight = 19785.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080938 restraints weight = 13755.275| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 15516 Z= 0.398 Angle : 0.795 9.765 21039 Z= 0.387 Chirality : 0.046 0.242 2604 Planarity : 0.005 0.066 2514 Dihedral : 6.987 43.935 3903 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.86 % Allowed : 17.09 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1731 helix: 1.17 (0.29), residues: 372 sheet: -0.10 (0.26), residues: 408 loop : -1.23 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 52 HIS 0.007 0.002 HIS a 305 PHE 0.043 0.003 PHE K 99 TYR 0.015 0.002 TYR H 110 ARG 0.013 0.001 ARG l 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3171.10 seconds wall clock time: 59 minutes 4.52 seconds (3544.52 seconds total)