Starting phenix.real_space_refine on Thu Feb 22 08:17:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/02_2024/7mw5_24063.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/02_2024/7mw5_24063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/02_2024/7mw5_24063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/02_2024/7mw5_24063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/02_2024/7mw5_24063.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/02_2024/7mw5_24063.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 149 5.16 5 C 21357 2.51 5 N 5503 2.21 5 O 6626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 194": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33635 Number of models: 1 Model: "" Number of chains: 41 Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1541 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8149 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8140 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8140 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8320 Chain: "B" Number of atoms: 8145 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8315 Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1541 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 8145 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8315 Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 843 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 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: "l" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN C1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 Time building chain proxies: 29.00, per 1000 atoms: 0.86 Number of scatterers: 33635 At special positions: 0 Unit cell: (164.472, 163.404, 248.844, 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 149 16.00 O 6626 8.00 N 5503 7.00 C 21357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 245 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 245 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 331 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 234 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 61 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 61 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 234 " " NAG I 1 " - " ASN C 282 " " NAG J 1 " - " ASN C 125 " " NAG K 1 " - " ASN C 331 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 343 " " NAG S 1 " - " ASN C 17 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 331 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B 717 " " NAG Z 1 " - " ASN B 709 " " NAG a 1 " - " ASN B 343 " " NAG b 1 " - " ASN B 17 " " NAG c 1 " - " ASN A 61 " " NAG d 1 " - " ASN A 282 " " NAG e 1 " - " ASN A 125 " " NAG f 1 " - " ASN A1134 " " NAG g 1 " - " ASN A1098 " " NAG h 1 " - " ASN A 801 " " NAG i 1 " - " ASN A 717 " " NAG j 1 " - " ASN A 709 " " NAG k 1 " - " ASN A 343 " " NAG l 1 " - " ASN A 17 " NAG-THR " NAG B1306 " - " THR B 124 " Time building additional restraints: 14.01 Conformation dependent library (CDL) restraints added in 10.6 seconds 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7912 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 77 sheets defined 18.9% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'L' and resid 50 through 54 Processing helix chain 'L' and resid 172 through 178 Processing helix chain 'L' and resid 234 through 239 Processing helix chain 'H' and resid 81 through 84 Processing helix chain 'H' and resid 237 through 242 removed outlier: 3.834A pdb=" N THR H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.927A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.511A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.784A pdb=" N LEU C 441 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C 442 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.528A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.364A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 941 removed outlier: 6.011A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.579A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.875A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.191A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.596A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.663A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.309A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 removed outlier: 3.715A pdb=" N TYR B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.093A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 921 through 941 removed outlier: 5.878A pdb=" N PHE B 927 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.755A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.537A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 172 through 179 removed outlier: 3.648A pdb=" N SER G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY G 179 " --> pdb=" O GLN G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 removed outlier: 4.107A pdb=" N HIS G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.908A pdb=" N GLY F 240 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.822A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.090A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.791A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.661A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.930A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.062A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 907 removed outlier: 3.610A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.353A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.600A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.548A pdb=" N THR E 54 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.570A pdb=" N PHE L 95 " --> pdb=" O CYS L 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'L' and resid 69 through 72 removed outlier: 6.509A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 69 through 72 removed outlier: 6.509A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 165 through 169 Processing sheet with id=AA6, first strand: chain 'L' and resid 205 through 206 removed outlier: 4.785A pdb=" N TRP L 199 " --> pdb=" O GLN L 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.566A pdb=" N CYS H 41 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA H 98 " --> pdb=" O CYS H 41 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR H 88 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.676A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.694A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.694A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 201 through 204 removed outlier: 4.512A pdb=" N TYR H 244 " --> pdb=" O VAL H 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.915A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.847A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.158A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.836A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 144 removed outlier: 6.080A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.466A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 325 through 326 removed outlier: 4.895A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.990A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.857A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.814A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 721 through 728 removed outlier: 7.078A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 721 through 728 Processing sheet with id=AC8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 790 removed outlier: 3.561A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AD2, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AD3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.917A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.070A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.601A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.114A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 196 through 197 Processing sheet with id=AD8, first strand: chain 'B' and resid 309 through 317 removed outlier: 6.599A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.741A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.569A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.388A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'B' and resid 721 through 728 removed outlier: 6.851A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.415A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.619A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 1080 through 1082 Processing sheet with id=AE9, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AF1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AF3, first strand: chain 'G' and resid 30 through 33 Processing sheet with id=AF4, first strand: chain 'G' and resid 69 through 70 Processing sheet with id=AF5, first strand: chain 'G' and resid 165 through 169 removed outlier: 3.847A pdb=" N SER G 165 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER G 182 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU G 232 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL G 184 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU G 230 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU G 186 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER G 228 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN G 188 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU G 226 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER G 225 " --> pdb=" O THR G 215 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 195 through 201 Processing sheet with id=AF7, first strand: chain 'F' and resid 24 through 26 removed outlier: 3.672A pdb=" N CYS F 41 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 98 " --> pdb=" O CYS F 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR F 99 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR F 90 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 101 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS F 86 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 77 through 79 removed outlier: 5.935A pdb=" N TRP F 66 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS F 57 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE F 70 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET F 53 " --> pdb=" O ILE F 70 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 170 through 174 removed outlier: 5.879A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 170 through 174 removed outlier: 5.879A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 201 through 204 Processing sheet with id=AG3, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.754A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.649A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.270A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AG7, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.746A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.278A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.009A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.571A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AH3, first strand: chain 'A' and resid 721 through 728 removed outlier: 6.827A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 721 through 728 Processing sheet with id=AH5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AH6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AH7, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AH8, first strand: chain 'A' and resid 1093 through 1097 Processing sheet with id=AH9, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AI1, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.574A pdb=" N GLU E 129 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.500A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AI4, first strand: chain 'D' and resid 77 through 79 removed outlier: 5.903A pdb=" N TRP D 66 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS D 57 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 70 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 53 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR D 127 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 87 through 92 1176 hydrogen bonds defined for protein. 3159 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: 15.37 Time building geometry restraints manager: 15.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10570 1.34 - 1.46: 7950 1.46 - 1.58: 15670 1.58 - 1.70: 0 1.70 - 1.82: 194 Bond restraints: 34384 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.18: 534 104.18 - 111.70: 16554 111.70 - 119.21: 11351 119.21 - 126.73: 17981 126.73 - 134.25: 404 Bond angle restraints: 46824 Sorted by residual: angle pdb=" C ALA B1070 " pdb=" N GLN B1071 " pdb=" CA GLN B1071 " ideal model delta sigma weight residual 121.33 128.42 -7.09 1.40e+00 5.10e-01 2.57e+01 angle pdb=" C LEU C 212 " pdb=" CA LEU C 212 " pdb=" CB LEU C 212 " ideal model delta sigma weight residual 115.79 110.12 5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" CA CYS H 115 " pdb=" CB CYS H 115 " pdb=" SG CYS H 115 " ideal model delta sigma weight residual 114.40 124.95 -10.55 2.30e+00 1.89e-01 2.11e+01 angle pdb=" N ALA B1070 " pdb=" CA ALA B1070 " pdb=" C ALA B1070 " ideal model delta sigma weight residual 107.32 114.80 -7.48 1.65e+00 3.67e-01 2.06e+01 angle pdb=" C LYS B1086 " pdb=" N ALA B1087 " pdb=" CA ALA B1087 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.70e+01 ... (remaining 46819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 20157 25.03 - 50.06: 985 50.06 - 75.08: 201 75.08 - 100.11: 120 100.11 - 125.14: 82 Dihedral angle restraints: 21545 sinusoidal: 9232 harmonic: 12313 Sorted by residual: dihedral pdb=" CA SER E 27 " pdb=" C SER E 27 " pdb=" N PRO E 28 " pdb=" CA PRO E 28 " ideal model delta harmonic sigma weight residual -180.00 -113.36 -66.64 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA SER G 27 " pdb=" C SER G 27 " pdb=" N PRO G 28 " pdb=" CA PRO G 28 " ideal model delta harmonic sigma weight residual -180.00 -114.49 -65.51 0 5.00e+00 4.00e-02 1.72e+02 dihedral pdb=" CA SER L 27 " pdb=" C SER L 27 " pdb=" N PRO L 28 " pdb=" CA PRO L 28 " ideal model delta harmonic sigma weight residual -180.00 -116.42 -63.58 0 5.00e+00 4.00e-02 1.62e+02 ... (remaining 21542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.255: 5559 0.255 - 0.510: 10 0.510 - 0.764: 3 0.764 - 1.019: 0 1.019 - 1.274: 1 Chirality restraints: 5573 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.45e+00 ... (remaining 5570 not shown) Planarity restraints: 5979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " 0.032 2.00e-02 2.50e+03 2.93e-02 1.07e+01 pdb=" CG ASN A 17 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS L 100 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO L 101 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO L 101 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 101 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 27 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C SER G 27 " -0.055 2.00e-02 2.50e+03 pdb=" O SER G 27 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO G 28 " 0.019 2.00e-02 2.50e+03 ... (remaining 5976 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 993 2.69 - 3.24: 33937 3.24 - 3.80: 53864 3.80 - 4.35: 71608 4.35 - 4.90: 115515 Nonbonded interactions: 275917 Sorted by model distance: nonbonded pdb=" OD2 ASP C 796 " pdb=" O6 NAG Z 1 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR G 60 " pdb=" O ARG F 119 " model vdw 2.166 2.440 nonbonded pdb=" NE2 GLN D 25 " pdb=" O TYR D 113 " model vdw 2.168 2.520 nonbonded pdb=" ND2 ASN F 54 " pdb=" O SER F 118 " model vdw 2.169 2.520 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.178 2.440 ... (remaining 275912 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' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1308)) selection = (chain 'B' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1308)) selection = (chain 'C' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1308)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.060 Check model and map are aligned: 0.500 Set scattering table: 0.280 Process input model: 106.490 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.004 0.102 34384 Z= 0.272 Angle : 0.729 10.555 46824 Z= 0.386 Chirality : 0.053 1.274 5573 Planarity : 0.005 0.082 5929 Dihedral : 18.472 125.138 13489 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.96 % Favored : 91.47 % Rotamer: Outliers : 0.11 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 4193 helix: 0.78 (0.20), residues: 670 sheet: -0.95 (0.16), residues: 1064 loop : -1.99 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 55 HIS 0.004 0.001 HIS L 100 PHE 0.027 0.002 PHE C 906 TYR 0.020 0.001 TYR C 505 ARG 0.007 0.000 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 53 MET cc_start: 0.8574 (mtt) cc_final: 0.8272 (mtt) REVERT: C 248 TYR cc_start: 0.4625 (m-10) cc_final: 0.4235 (m-10) REVERT: F 84 LYS cc_start: 0.7060 (mmtt) cc_final: 0.6568 (mmmt) REVERT: F 100 MET cc_start: 0.7461 (mmp) cc_final: 0.7159 (mmt) REVERT: F 204 TRP cc_start: 0.5670 (m100) cc_final: 0.5379 (m100) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.4253 time to fit residues: 162.1480 Evaluate side-chains 159 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 176 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 328 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 199 optimal weight: 0.2980 chunk 244 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 HIS L 175 GLN ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS H 247 ASN H 249 ASN C 69 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN B 641 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN G 211 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 901 GLN A 919 ASN E 26 GLN E 100 HIS ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34384 Z= 0.256 Angle : 0.723 14.185 46824 Z= 0.356 Chirality : 0.053 0.933 5573 Planarity : 0.005 0.062 5929 Dihedral : 16.404 113.987 6264 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.58 % Favored : 90.87 % Rotamer: Outliers : 0.70 % Allowed : 4.63 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 4193 helix: 1.13 (0.20), residues: 670 sheet: -0.88 (0.16), residues: 1080 loop : -1.98 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 59 HIS 0.011 0.001 HIS C 69 PHE 0.030 0.002 PHE C 906 TYR 0.027 0.002 TYR B 265 ARG 0.016 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 216 GLU cc_start: 0.8106 (pp20) cc_final: 0.7905 (pp20) REVERT: H 53 MET cc_start: 0.8574 (mtt) cc_final: 0.8320 (mtt) REVERT: B 157 PHE cc_start: 0.8468 (p90) cc_final: 0.8251 (p90) REVERT: F 100 MET cc_start: 0.7716 (mmp) cc_final: 0.7506 (mmm) REVERT: F 109 ASP cc_start: 0.7781 (t0) cc_final: 0.7334 (t0) REVERT: F 122 TYR cc_start: 0.6007 (t80) cc_final: 0.5615 (t80) REVERT: F 204 TRP cc_start: 0.5706 (m100) cc_final: 0.5461 (m100) REVERT: A 68 ILE cc_start: 0.6670 (mm) cc_final: 0.6223 (mt) REVERT: E 40 THR cc_start: 0.6156 (m) cc_final: 0.5790 (m) REVERT: E 107 ILE cc_start: 0.6042 (mm) cc_final: 0.5829 (mm) REVERT: D 82 LYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5632 (ptpt) outliers start: 23 outliers final: 15 residues processed: 193 average time/residue: 0.4154 time to fit residues: 136.5996 Evaluate side-chains 171 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 82 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 381 optimal weight: 1.9990 chunk 411 optimal weight: 10.0000 chunk 339 optimal weight: 0.1980 chunk 378 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 189 ASN ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS H 247 ASN C 69 HIS C 954 GLN B 641 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN G 58 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34384 Z= 0.196 Angle : 0.683 16.243 46824 Z= 0.333 Chirality : 0.051 0.827 5573 Planarity : 0.005 0.062 5929 Dihedral : 14.924 113.801 6264 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.98 % Favored : 91.52 % Rotamer: Outliers : 0.76 % Allowed : 6.96 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 4193 helix: 1.34 (0.20), residues: 673 sheet: -0.85 (0.16), residues: 1069 loop : -1.91 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 59 HIS 0.030 0.001 HIS C 69 PHE 0.026 0.002 PHE L 169 TYR 0.023 0.001 TYR C 369 ARG 0.010 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 190 PHE cc_start: 0.8514 (p90) cc_final: 0.8250 (p90) REVERT: H 39 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8649 (mm) REVERT: H 100 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (tpt) REVERT: H 249 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.7941 (t0) REVERT: B 157 PHE cc_start: 0.8506 (p90) cc_final: 0.8251 (p90) REVERT: G 58 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: F 100 MET cc_start: 0.7547 (mmp) cc_final: 0.7339 (mmm) REVERT: F 109 ASP cc_start: 0.7692 (t0) cc_final: 0.6575 (p0) REVERT: F 113 TYR cc_start: 0.7623 (m-80) cc_final: 0.7394 (m-10) REVERT: F 204 TRP cc_start: 0.5795 (m100) cc_final: 0.5485 (m100) REVERT: A 68 ILE cc_start: 0.6650 (mm) cc_final: 0.6215 (mt) REVERT: E 40 THR cc_start: 0.6088 (m) cc_final: 0.5837 (m) REVERT: E 107 ILE cc_start: 0.5953 (mm) cc_final: 0.5682 (mm) outliers start: 25 outliers final: 14 residues processed: 192 average time/residue: 0.4494 time to fit residues: 146.8387 Evaluate side-chains 169 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 169 PHE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 0.7980 chunk 286 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 181 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 382 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS H 247 ASN C 69 HIS C 388 ASN C 954 GLN B 641 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34384 Z= 0.210 Angle : 0.675 14.663 46824 Z= 0.329 Chirality : 0.050 0.811 5573 Planarity : 0.005 0.060 5929 Dihedral : 13.970 114.295 6264 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.58 % Favored : 91.01 % Rotamer: Outliers : 0.79 % Allowed : 8.75 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 4193 helix: 1.43 (0.20), residues: 671 sheet: -0.85 (0.16), residues: 1074 loop : -1.86 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 59 HIS 0.019 0.001 HIS C 69 PHE 0.023 0.002 PHE L 169 TYR 0.027 0.001 TYR A 473 ARG 0.004 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8639 (mm) REVERT: H 249 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.7922 (t0) REVERT: B 157 PHE cc_start: 0.8500 (p90) cc_final: 0.8277 (p90) REVERT: B 513 LEU cc_start: 0.7742 (tp) cc_final: 0.7486 (tp) REVERT: F 109 ASP cc_start: 0.7743 (t0) cc_final: 0.6554 (p0) REVERT: F 113 TYR cc_start: 0.7558 (m-80) cc_final: 0.7318 (m-10) REVERT: F 204 TRP cc_start: 0.5801 (m100) cc_final: 0.5529 (m100) REVERT: A 68 ILE cc_start: 0.6675 (mm) cc_final: 0.6246 (mt) REVERT: E 40 THR cc_start: 0.6218 (m) cc_final: 0.5955 (m) REVERT: E 106 ASP cc_start: 0.7517 (t0) cc_final: 0.7190 (t70) REVERT: E 107 ILE cc_start: 0.5967 (mm) cc_final: 0.5659 (mm) outliers start: 26 outliers final: 18 residues processed: 186 average time/residue: 0.4148 time to fit residues: 135.0475 Evaluate side-chains 173 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 169 PHE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 301 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 345 optimal weight: 3.9990 chunk 279 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 189 ASN ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS H 247 ASN C 69 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN B 641 ASN B1005 GLN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 34384 Z= 0.429 Angle : 0.776 15.260 46824 Z= 0.381 Chirality : 0.054 0.923 5573 Planarity : 0.005 0.059 5929 Dihedral : 13.497 116.826 6264 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.13 % Favored : 89.44 % Rotamer: Outliers : 1.15 % Allowed : 10.41 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 4193 helix: 1.12 (0.20), residues: 662 sheet: -1.04 (0.16), residues: 1068 loop : -1.97 (0.12), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 55 HIS 0.031 0.002 HIS C 69 PHE 0.029 0.003 PHE C 906 TYR 0.022 0.002 TYR B 265 ARG 0.010 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 167 PHE cc_start: 0.4199 (t80) cc_final: 0.3887 (t80) REVERT: B 157 PHE cc_start: 0.8494 (p90) cc_final: 0.8289 (p90) REVERT: B 513 LEU cc_start: 0.7674 (tp) cc_final: 0.7430 (tp) REVERT: G 70 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8399 (t) REVERT: F 125 GLN cc_start: 0.7976 (pp30) cc_final: 0.7213 (mm-40) REVERT: F 204 TRP cc_start: 0.6034 (m100) cc_final: 0.5696 (m100) REVERT: A 68 ILE cc_start: 0.6740 (mm) cc_final: 0.6329 (mt) REVERT: E 106 ASP cc_start: 0.7653 (t0) cc_final: 0.7261 (t70) REVERT: E 107 ILE cc_start: 0.5949 (mm) cc_final: 0.5623 (mm) REVERT: D 74 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7095 (p) outliers start: 39 outliers final: 28 residues processed: 189 average time/residue: 0.4160 time to fit residues: 136.8218 Evaluate side-chains 179 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 169 PHE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 1.9990 chunk 364 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 405 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS B 641 ASN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34384 Z= 0.191 Angle : 0.672 14.749 46824 Z= 0.328 Chirality : 0.050 0.824 5573 Planarity : 0.005 0.060 5929 Dihedral : 12.644 117.250 6264 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.39 % Favored : 91.23 % Rotamer: Outliers : 1.07 % Allowed : 11.28 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 4193 helix: 1.41 (0.20), residues: 665 sheet: -0.98 (0.16), residues: 1087 loop : -1.84 (0.12), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 55 HIS 0.029 0.001 HIS C 69 PHE 0.029 0.002 PHE D 48 TYR 0.031 0.001 TYR A 473 ARG 0.005 0.000 ARG F 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 3.810 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: H 100 MET cc_start: 0.8444 (ttp) cc_final: 0.7792 (tpt) REVERT: B 513 LEU cc_start: 0.7672 (tp) cc_final: 0.7438 (tp) REVERT: F 100 MET cc_start: 0.6256 (mmm) cc_final: 0.6047 (mmt) REVERT: F 109 ASP cc_start: 0.7568 (t0) cc_final: 0.7305 (t0) REVERT: F 113 TYR cc_start: 0.7723 (m-80) cc_final: 0.7472 (m-10) REVERT: F 125 GLN cc_start: 0.8001 (pp30) cc_final: 0.7327 (mm-40) REVERT: F 204 TRP cc_start: 0.6008 (m100) cc_final: 0.5617 (m100) REVERT: A 68 ILE cc_start: 0.6598 (mm) cc_final: 0.6191 (mt) REVERT: E 40 THR cc_start: 0.6442 (m) cc_final: 0.6207 (m) REVERT: E 94 ASP cc_start: 0.7454 (t0) cc_final: 0.7251 (t70) REVERT: E 106 ASP cc_start: 0.7599 (t0) cc_final: 0.7201 (t70) REVERT: E 107 ILE cc_start: 0.5977 (mm) cc_final: 0.5646 (mm) REVERT: E 127 LYS cc_start: 0.7169 (pptt) cc_final: 0.6603 (pptt) outliers start: 36 outliers final: 27 residues processed: 194 average time/residue: 0.4245 time to fit residues: 142.1977 Evaluate side-chains 180 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 390 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 230 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 341 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 403 optimal weight: 0.0670 chunk 252 optimal weight: 0.0670 chunk 246 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 GLN ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS G 58 GLN F 22 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34384 Z= 0.167 Angle : 0.649 14.389 46824 Z= 0.317 Chirality : 0.049 0.768 5573 Planarity : 0.005 0.060 5929 Dihedral : 11.914 117.032 6264 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.15 % Favored : 91.47 % Rotamer: Outliers : 1.01 % Allowed : 11.90 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 4193 helix: 1.59 (0.20), residues: 664 sheet: -0.87 (0.16), residues: 1095 loop : -1.76 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 55 HIS 0.015 0.001 HIS H 214 PHE 0.029 0.001 PHE B 157 TYR 0.023 0.001 TYR E 73 ARG 0.007 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 MET cc_start: 0.8348 (ttp) cc_final: 0.7807 (tpt) REVERT: H 249 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.7829 (t0) REVERT: B 456 PHE cc_start: 0.7584 (m-10) cc_final: 0.7159 (m-10) REVERT: B 489 TYR cc_start: 0.8366 (p90) cc_final: 0.8140 (p90) REVERT: B 513 LEU cc_start: 0.7823 (tp) cc_final: 0.7533 (tp) REVERT: G 73 TYR cc_start: 0.6143 (m-10) cc_final: 0.5869 (m-80) REVERT: F 109 ASP cc_start: 0.7593 (t0) cc_final: 0.7296 (t0) REVERT: F 125 GLN cc_start: 0.7958 (pp30) cc_final: 0.7383 (mm-40) REVERT: F 204 TRP cc_start: 0.5999 (m100) cc_final: 0.5637 (m100) REVERT: A 68 ILE cc_start: 0.6706 (mm) cc_final: 0.6320 (mt) REVERT: A 338 PHE cc_start: 0.7118 (t80) cc_final: 0.6884 (t80) REVERT: E 40 THR cc_start: 0.6410 (m) cc_final: 0.6201 (m) REVERT: E 106 ASP cc_start: 0.7608 (t0) cc_final: 0.7216 (t70) REVERT: E 107 ILE cc_start: 0.5975 (mm) cc_final: 0.5619 (mm) REVERT: E 127 LYS cc_start: 0.7156 (pptt) cc_final: 0.6548 (pptt) REVERT: D 100 MET cc_start: 0.6493 (tmm) cc_final: 0.5912 (tmm) outliers start: 34 outliers final: 26 residues processed: 200 average time/residue: 0.4319 time to fit residues: 146.3592 Evaluate side-chains 183 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 249 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 275 optimal weight: 9.9990 chunk 199 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 chunk 317 optimal weight: 1.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS B 641 ASN B 901 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34384 Z= 0.180 Angle : 0.647 11.472 46824 Z= 0.316 Chirality : 0.049 0.752 5573 Planarity : 0.005 0.059 5929 Dihedral : 11.632 116.698 6264 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.56 % Favored : 91.09 % Rotamer: Outliers : 1.12 % Allowed : 12.09 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4193 helix: 1.65 (0.20), residues: 663 sheet: -0.87 (0.16), residues: 1092 loop : -1.74 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 55 HIS 0.010 0.001 HIS H 214 PHE 0.030 0.001 PHE B 157 TYR 0.042 0.001 TYR A 473 ARG 0.005 0.000 ARG F 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 3.578 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: H 100 MET cc_start: 0.8104 (ttp) cc_final: 0.7596 (tpt) REVERT: H 249 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.7827 (t0) REVERT: B 456 PHE cc_start: 0.7622 (m-10) cc_final: 0.7159 (m-10) REVERT: B 489 TYR cc_start: 0.8370 (p90) cc_final: 0.7994 (p90) REVERT: F 109 ASP cc_start: 0.7533 (t0) cc_final: 0.7300 (t0) REVERT: F 113 TYR cc_start: 0.7823 (m-80) cc_final: 0.7560 (m-10) REVERT: F 125 GLN cc_start: 0.7907 (pp30) cc_final: 0.7335 (mm-40) REVERT: F 204 TRP cc_start: 0.6018 (m100) cc_final: 0.5669 (m100) REVERT: A 68 ILE cc_start: 0.6717 (mm) cc_final: 0.6340 (mt) REVERT: A 338 PHE cc_start: 0.7122 (t80) cc_final: 0.6895 (t80) REVERT: E 40 THR cc_start: 0.6362 (m) cc_final: 0.6154 (m) REVERT: E 106 ASP cc_start: 0.7603 (t0) cc_final: 0.7207 (t70) REVERT: E 107 ILE cc_start: 0.5949 (mm) cc_final: 0.5591 (mm) REVERT: E 127 LYS cc_start: 0.7210 (pptt) cc_final: 0.6607 (pptt) REVERT: D 55 TRP cc_start: 0.7606 (m100) cc_final: 0.7191 (m100) REVERT: D 100 MET cc_start: 0.6711 (tmm) cc_final: 0.5728 (tmm) outliers start: 38 outliers final: 31 residues processed: 193 average time/residue: 0.4084 time to fit residues: 136.0360 Evaluate side-chains 187 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 367 optimal weight: 1.9990 chunk 386 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 376 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 295 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 340 optimal weight: 6.9990 chunk 355 optimal weight: 4.9990 chunk 375 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34384 Z= 0.237 Angle : 0.667 15.249 46824 Z= 0.326 Chirality : 0.050 0.776 5573 Planarity : 0.005 0.060 5929 Dihedral : 11.488 116.332 6264 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.08 % Favored : 90.56 % Rotamer: Outliers : 1.12 % Allowed : 12.18 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 4193 helix: 1.57 (0.20), residues: 663 sheet: -0.89 (0.16), residues: 1047 loop : -1.77 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 199 HIS 0.004 0.001 HIS C1083 PHE 0.032 0.002 PHE B 157 TYR 0.024 0.001 TYR E 73 ARG 0.004 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 MET cc_start: 0.7982 (ttp) cc_final: 0.7393 (tpt) REVERT: B 456 PHE cc_start: 0.7663 (m-10) cc_final: 0.7155 (m-10) REVERT: B 489 TYR cc_start: 0.8268 (p90) cc_final: 0.7962 (p90) REVERT: F 125 GLN cc_start: 0.7938 (pp30) cc_final: 0.7407 (mm-40) REVERT: F 204 TRP cc_start: 0.6141 (m100) cc_final: 0.5771 (m100) REVERT: A 68 ILE cc_start: 0.6718 (mm) cc_final: 0.6353 (mt) REVERT: A 338 PHE cc_start: 0.7115 (t80) cc_final: 0.6887 (t80) REVERT: E 40 THR cc_start: 0.6496 (m) cc_final: 0.6293 (m) REVERT: E 94 ASP cc_start: 0.7441 (t0) cc_final: 0.7211 (t0) REVERT: E 107 ILE cc_start: 0.6144 (mm) cc_final: 0.5777 (mm) REVERT: E 109 MET cc_start: 0.8057 (tpt) cc_final: 0.7545 (mmm) REVERT: E 127 LYS cc_start: 0.7225 (pptt) cc_final: 0.6441 (pptt) outliers start: 38 outliers final: 35 residues processed: 184 average time/residue: 0.3877 time to fit residues: 125.5544 Evaluate side-chains 182 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 247 optimal weight: 2.9990 chunk 397 optimal weight: 20.0000 chunk 242 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 276 optimal weight: 5.9990 chunk 417 optimal weight: 0.1980 chunk 384 optimal weight: 0.5980 chunk 332 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 256 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34384 Z= 0.176 Angle : 0.644 12.570 46824 Z= 0.315 Chirality : 0.049 0.745 5573 Planarity : 0.005 0.063 5929 Dihedral : 11.217 116.059 6264 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.17 % Favored : 91.47 % Rotamer: Outliers : 1.04 % Allowed : 12.43 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 4193 helix: 1.67 (0.20), residues: 662 sheet: -0.82 (0.16), residues: 1058 loop : -1.71 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 55 HIS 0.004 0.001 HIS C1083 PHE 0.030 0.001 PHE L 167 TYR 0.025 0.001 TYR E 73 ARG 0.005 0.000 ARG D 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 MET cc_start: 0.7795 (ttp) cc_final: 0.7421 (tpt) REVERT: B 456 PHE cc_start: 0.7647 (m-10) cc_final: 0.7184 (m-10) REVERT: B 489 TYR cc_start: 0.8285 (p90) cc_final: 0.7998 (p90) REVERT: F 109 ASP cc_start: 0.7182 (t0) cc_final: 0.6395 (p0) REVERT: F 204 TRP cc_start: 0.6116 (m100) cc_final: 0.5760 (m100) REVERT: A 68 ILE cc_start: 0.6631 (mm) cc_final: 0.6302 (mt) REVERT: A 338 PHE cc_start: 0.7031 (t80) cc_final: 0.6808 (t80) REVERT: E 94 ASP cc_start: 0.7422 (t0) cc_final: 0.7196 (t70) REVERT: E 107 ILE cc_start: 0.6101 (mm) cc_final: 0.5776 (mm) REVERT: E 109 MET cc_start: 0.8107 (tpt) cc_final: 0.7608 (mmm) REVERT: E 127 LYS cc_start: 0.7250 (pptt) cc_final: 0.6472 (pptt) outliers start: 35 outliers final: 32 residues processed: 192 average time/residue: 0.4055 time to fit residues: 137.0258 Evaluate side-chains 186 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 4.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 264 optimal weight: 5.9990 chunk 354 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 306 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 332 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 341 optimal weight: 10.0000 chunk 42 optimal weight: 0.0060 chunk 61 optimal weight: 8.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 HIS ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.080332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.058912 restraints weight = 293508.084| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 5.29 r_work: 0.3011 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 34384 Z= 0.332 Angle : 0.711 16.689 46824 Z= 0.349 Chirality : 0.051 0.820 5573 Planarity : 0.005 0.064 5929 Dihedral : 11.375 115.491 6264 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.56 % Favored : 90.11 % Rotamer: Outliers : 1.07 % Allowed : 12.60 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 4193 helix: 1.40 (0.20), residues: 666 sheet: -0.94 (0.16), residues: 1049 loop : -1.80 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 55 HIS 0.006 0.001 HIS C1048 PHE 0.030 0.002 PHE B 79 TYR 0.024 0.002 TYR E 73 ARG 0.007 0.001 ARG B 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6470.55 seconds wall clock time: 119 minutes 41.33 seconds (7181.33 seconds total)