Starting phenix.real_space_refine on Thu Feb 22 10:14:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw2_24060/02_2024/7mw2_24060.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw2_24060/02_2024/7mw2_24060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw2_24060/02_2024/7mw2_24060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw2_24060/02_2024/7mw2_24060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw2_24060/02_2024/7mw2_24060.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw2_24060/02_2024/7mw2_24060.pdb" } resolution = 2.97 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 147 5.16 5 C 21459 2.51 5 N 5529 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33807 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "E" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "G" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 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 Time building chain proxies: 28.51, per 1000 atoms: 0.84 Number of scatterers: 33807 At special positions: 0 Unit cell: (138.84, 140.976, 222.144, 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 147 16.00 O 6672 8.00 N 5529 7.00 C 21459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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 738 " - pdb=" SG CYS A 760 " 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=2.03 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 220 " distance=2.04 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 391 " - pdb=" SG CYS C 525 " 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=2.04 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 738 " - pdb=" SG CYS C 760 " 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 L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 220 " 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=2.04 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 738 " - pdb=" SG CYS B 760 " 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 158 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 164 " - pdb=" SG CYS F 220 " 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-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 61 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 125 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A1074 " " 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 B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 125 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1074 " " 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 C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 125 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C1074 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 234 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN B1134 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B 709 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 343 " Time building additional restraints: 13.86 Conformation dependent library (CDL) restraints added in 9.9 seconds 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8028 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 79 sheets defined 20.6% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.061A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.597A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.692A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.217A 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 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.566A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.713A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.131A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.601A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 1033 removed outlier: 3.890A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.742A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.072A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.625A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.789A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.240A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.638A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.709A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.558A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.251A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.586A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.818A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.793A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'L' and resid 207 through 211 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 211 through 214 removed outlier: 4.295A pdb=" N GLY H 214 " --> pdb=" O SER H 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 211 through 214' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.026A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.751A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.754A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.720A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.106A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) 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: 3.647A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.744A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.207A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.601A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 removed outlier: 3.509A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.884A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.849A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 207 through 211 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 211 through 214 removed outlier: 4.188A pdb=" N GLY F 214 " --> pdb=" O SER F 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 211 through 214' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.700A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.220A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.188A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.509A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.965A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 319 removed outlier: 5.767A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 5.248A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.733A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.878A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.532A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.164A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'E' and resid 24 through 27 Processing sheet with id=AC2, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.386A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.386A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 121 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 138 through 142 removed outlier: 6.080A pdb=" N TYR E 197 " --> pdb=" O ASN E 162 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER E 198 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AC6, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AC7, first strand: chain 'D' and resid 29 through 31 removed outlier: 5.003A pdb=" N ALA D 125 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY D 119 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TRP D 127 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG D 117 " --> pdb=" O TRP D 127 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN D 129 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS D 115 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET D 53 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.030A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.030A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.254A pdb=" N TYR D 218 " --> pdb=" O VAL D 235 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.822A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.036A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.363A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.993A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 312 through 319 removed outlier: 6.030A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.239A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.751A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.561A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.152A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AF1, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.286A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.286A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AF4, first strand: chain 'L' and resid 138 through 142 removed outlier: 5.948A pdb=" N TYR L 197 " --> pdb=" O ASN L 162 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER L 198 " --> pdb=" O THR L 188 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 177 through 178 Processing sheet with id=AF6, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AF7, first strand: chain 'H' and resid 29 through 31 removed outlier: 4.995A pdb=" N ALA H 125 " --> pdb=" O GLY H 119 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY H 119 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TRP H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG H 117 " --> pdb=" O TRP H 127 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN H 129 " --> pdb=" O CYS H 115 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS H 115 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.066A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.066A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 175 through 178 removed outlier: 4.172A pdb=" N TYR H 218 " --> pdb=" O VAL H 235 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.781A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AG4, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.053A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.356A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.849A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 312 through 319 removed outlier: 5.925A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.693A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AG9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AH1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AH2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.844A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.377A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.377A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.186A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AH7, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AH8, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.263A pdb=" N LEU G 31 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.263A pdb=" N LEU G 31 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR G 121 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 138 through 142 removed outlier: 6.070A pdb=" N TYR G 197 " --> pdb=" O ASN G 162 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G 198 " --> pdb=" O THR G 188 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 168 through 174 Processing sheet with id=AI3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AI4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.993A pdb=" N ALA F 125 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY F 119 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TRP F 127 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG F 117 " --> pdb=" O TRP F 127 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN F 129 " --> pdb=" O CYS F 115 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS F 115 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET F 53 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR F 69 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.126A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.126A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 175 through 178 removed outlier: 4.218A pdb=" N TYR F 218 " --> pdb=" O VAL F 235 " (cutoff:3.500A) 1495 hydrogen bonds defined for protein. 4056 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: 17.23 Time building geometry restraints manager: 15.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9292 1.33 - 1.46: 7322 1.46 - 1.58: 17766 1.58 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 34569 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 34564 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.76: 856 105.76 - 112.81: 18787 112.81 - 119.87: 10262 119.87 - 126.92: 16869 126.92 - 133.98: 347 Bond angle restraints: 47121 Sorted by residual: angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 111.77 103.74 8.03 1.04e+00 9.25e-01 5.96e+01 angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 111.77 104.57 7.20 1.04e+00 9.25e-01 4.79e+01 angle pdb=" N GLY C 502 " pdb=" CA GLY C 502 " pdb=" C GLY C 502 " ideal model delta sigma weight residual 111.93 106.87 5.06 1.15e+00 7.56e-01 1.93e+01 angle pdb=" N GLY A 502 " pdb=" CA GLY A 502 " pdb=" C GLY A 502 " ideal model delta sigma weight residual 111.93 107.12 4.81 1.15e+00 7.56e-01 1.75e+01 angle pdb=" C GLN A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.85 115.66 4.19 1.01e+00 9.80e-01 1.72e+01 ... (remaining 47116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 20399 25.94 - 51.89: 818 51.89 - 77.83: 152 77.83 - 103.78: 64 103.78 - 129.72: 41 Dihedral angle restraints: 21474 sinusoidal: 8985 harmonic: 12489 Sorted by residual: 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 -108.14 -71.86 0 5.00e+00 4.00e-02 2.07e+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 -108.16 -71.84 0 5.00e+00 4.00e-02 2.06e+02 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 -108.38 -71.62 0 5.00e+00 4.00e-02 2.05e+02 ... (remaining 21471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.530: 5586 0.530 - 1.060: 3 1.060 - 1.590: 0 1.590 - 2.120: 2 2.120 - 2.650: 1 Chirality restraints: 5592 Sorted by residual: chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 0.25 -2.65 2.00e-01 2.50e+01 1.76e+02 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -0.61 -1.79 2.00e-01 2.50e+01 7.99e+01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -0.66 -1.74 2.00e-01 2.50e+01 7.54e+01 ... (remaining 5589 not shown) Planarity restraints: 6051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " 0.249 2.00e-02 2.50e+03 2.12e-01 5.61e+02 pdb=" C7 NAG A1309 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " -0.363 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.245 2.00e-02 2.50e+03 2.08e-01 5.40e+02 pdb=" C7 NAG B1309 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " 0.217 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C7 NAG C1310 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " -0.291 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " -0.022 2.00e-02 2.50e+03 ... (remaining 6048 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 4 2.23 - 2.89: 13237 2.89 - 3.56: 45476 3.56 - 4.23: 81907 4.23 - 4.90: 138772 Nonbonded interactions: 279396 Sorted by model distance: nonbonded pdb=" ND2 ASN B1074 " pdb=" C1 NAG B1310 " model vdw 1.558 3.550 nonbonded pdb=" ND2 ASN A1074 " pdb=" C1 NAG A1310 " model vdw 1.558 3.550 nonbonded pdb=" ND2 ASN C1074 " pdb=" C1 NAG C1310 " model vdw 1.570 3.550 nonbonded pdb=" OG SER C 591 " pdb=" OE2 GLU C 619 " model vdw 2.189 2.440 nonbonded pdb=" OD1 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.295 2.440 ... (remaining 279391 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 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = 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' } 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: 0.000 Normalize map: mean=0, sd=1: 5.460 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: 13.600 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 109.510 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.640 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:14.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 0.086 34569 Z= 0.286 Angle : 0.684 10.601 47121 Z= 0.371 Chirality : 0.073 2.650 5592 Planarity : 0.007 0.212 6003 Dihedral : 16.064 129.723 13293 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4233 helix: 0.52 (0.19), residues: 729 sheet: 0.56 (0.14), residues: 1323 loop : -0.83 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 PHE 0.024 0.002 PHE A 906 TYR 0.019 0.001 TYR E 73 ARG 0.006 0.000 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 306 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 MET cc_start: 0.7623 (tpt) cc_final: 0.7351 (tpp) REVERT: H 146 PHE cc_start: 0.6965 (m-10) cc_final: 0.6621 (m-10) REVERT: B 697 MET cc_start: 0.8578 (ptm) cc_final: 0.8226 (ptm) outliers start: 3 outliers final: 3 residues processed: 307 average time/residue: 1.3551 time to fit residues: 505.0100 Evaluate side-chains 231 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 0.9990 chunk 322 optimal weight: 0.0060 chunk 179 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 217 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 248 optimal weight: 0.0070 chunk 386 optimal weight: 5.9990 overall best weight: 0.9418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS C 901 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 901 GLN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34569 Z= 0.231 Angle : 0.658 11.217 47121 Z= 0.319 Chirality : 0.052 0.827 5592 Planarity : 0.005 0.062 6003 Dihedral : 13.147 103.737 6099 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.27 % Favored : 96.59 % Rotamer: Outliers : 1.61 % Allowed : 4.59 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4233 helix: 1.48 (0.20), residues: 705 sheet: 0.53 (0.14), residues: 1326 loop : -0.89 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.008 0.001 HIS D 188 PHE 0.031 0.002 PHE C 906 TYR 0.024 0.001 TYR B1067 ARG 0.009 0.000 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 244 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 146 PHE cc_start: 0.6896 (m-10) cc_final: 0.6691 (m-10) REVERT: B 314 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: B 697 MET cc_start: 0.8516 (ptm) cc_final: 0.8286 (ptm) REVERT: F 225 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7106 (tppp) outliers start: 55 outliers final: 25 residues processed: 276 average time/residue: 1.4479 time to fit residues: 481.3541 Evaluate side-chains 254 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 263 optimal weight: 7.9990 chunk 106 optimal weight: 0.0970 chunk 387 optimal weight: 0.0040 chunk 418 optimal weight: 5.9990 chunk 345 optimal weight: 0.7980 chunk 384 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 310 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34569 Z= 0.178 Angle : 0.619 12.591 47121 Z= 0.298 Chirality : 0.050 0.748 5592 Planarity : 0.004 0.059 6003 Dihedral : 11.593 96.720 6093 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.96 % Favored : 96.83 % Rotamer: Outliers : 1.58 % Allowed : 6.37 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4233 helix: 1.80 (0.20), residues: 705 sheet: 0.53 (0.14), residues: 1344 loop : -0.91 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 178 HIS 0.005 0.001 HIS H 188 PHE 0.032 0.001 PHE C 133 TYR 0.033 0.001 TYR C 904 ARG 0.007 0.000 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 142 PHE cc_start: 0.4889 (m-10) cc_final: 0.4530 (m-80) REVERT: H 146 PHE cc_start: 0.6857 (m-10) cc_final: 0.6595 (m-10) REVERT: B 314 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: B 697 MET cc_start: 0.8534 (ptm) cc_final: 0.8317 (ptm) REVERT: F 225 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7075 (tppp) outliers start: 54 outliers final: 23 residues processed: 269 average time/residue: 1.3611 time to fit residues: 443.6936 Evaluate side-chains 248 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 184 optimal weight: 0.7980 chunk 260 optimal weight: 20.0000 chunk 388 optimal weight: 0.6980 chunk 411 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 368 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34569 Z= 0.243 Angle : 0.643 11.544 47121 Z= 0.309 Chirality : 0.051 0.730 5592 Planarity : 0.004 0.060 6003 Dihedral : 10.797 94.630 6093 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.13 % Favored : 96.66 % Rotamer: Outliers : 1.61 % Allowed : 7.62 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 4233 helix: 1.86 (0.20), residues: 705 sheet: 0.48 (0.14), residues: 1344 loop : -0.91 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 178 HIS 0.003 0.001 HIS D 188 PHE 0.025 0.002 PHE B 906 TYR 0.020 0.001 TYR B1067 ARG 0.008 0.000 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 3.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 142 PHE cc_start: 0.4967 (m-10) cc_final: 0.4629 (m-80) REVERT: H 146 PHE cc_start: 0.6865 (m-80) cc_final: 0.6533 (m-10) REVERT: B 233 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5539 (pp) REVERT: B 314 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: B 697 MET cc_start: 0.8566 (ptm) cc_final: 0.8325 (ptm) REVERT: F 225 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7054 (tppp) outliers start: 55 outliers final: 31 residues processed: 260 average time/residue: 1.3844 time to fit residues: 436.5414 Evaluate side-chains 252 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 306 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 369 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN B 81 ASN B 134 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34569 Z= 0.272 Angle : 0.647 10.966 47121 Z= 0.313 Chirality : 0.051 0.767 5592 Planarity : 0.005 0.061 6003 Dihedral : 9.867 93.177 6093 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.56 % Rotamer: Outliers : 1.67 % Allowed : 8.28 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 4233 helix: 1.86 (0.20), residues: 705 sheet: 0.44 (0.14), residues: 1344 loop : -0.93 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 178 HIS 0.003 0.001 HIS A1064 PHE 0.024 0.002 PHE C 906 TYR 0.020 0.001 TYR B1067 ARG 0.008 0.000 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8429 (ptm) cc_final: 0.8171 (ptp) REVERT: L 142 PHE cc_start: 0.5218 (m-10) cc_final: 0.4886 (m-80) REVERT: H 129 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: H 146 PHE cc_start: 0.6862 (m-80) cc_final: 0.6556 (m-10) REVERT: H 225 LYS cc_start: 0.6930 (mppt) cc_final: 0.5600 (tptt) REVERT: B 233 ILE cc_start: 0.5900 (OUTLIER) cc_final: 0.5486 (pp) REVERT: B 314 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8179 (tm-30) outliers start: 57 outliers final: 32 residues processed: 263 average time/residue: 1.4076 time to fit residues: 448.9353 Evaluate side-chains 256 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 5.9990 chunk 370 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 241 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 412 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 136 optimal weight: 0.4980 chunk 216 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN B 926 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34569 Z= 0.203 Angle : 0.619 10.533 47121 Z= 0.297 Chirality : 0.049 0.676 5592 Planarity : 0.004 0.059 6003 Dihedral : 9.183 91.454 6093 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.13 % Favored : 96.66 % Rotamer: Outliers : 1.50 % Allowed : 8.87 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4233 helix: 1.97 (0.20), residues: 705 sheet: 0.43 (0.14), residues: 1308 loop : -0.88 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 178 HIS 0.003 0.001 HIS F 188 PHE 0.018 0.001 PHE C 133 TYR 0.019 0.001 TYR B1067 ARG 0.011 0.000 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 235 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8434 (ptm) cc_final: 0.8170 (ptp) REVERT: L 142 PHE cc_start: 0.5154 (m-10) cc_final: 0.4812 (m-80) REVERT: H 146 PHE cc_start: 0.6845 (m-80) cc_final: 0.6509 (m-10) REVERT: H 225 LYS cc_start: 0.6745 (mppt) cc_final: 0.5358 (tptp) REVERT: B 233 ILE cc_start: 0.5814 (OUTLIER) cc_final: 0.5376 (pp) REVERT: G 219 GLU cc_start: 0.6658 (tp30) cc_final: 0.6440 (tp30) REVERT: F 225 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.7017 (tppp) outliers start: 51 outliers final: 30 residues processed: 263 average time/residue: 1.3588 time to fit residues: 433.9605 Evaluate side-chains 256 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 300 optimal weight: 0.5980 chunk 233 optimal weight: 0.6980 chunk 346 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 410 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN B 926 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34569 Z= 0.223 Angle : 0.627 11.975 47121 Z= 0.304 Chirality : 0.050 0.699 5592 Planarity : 0.004 0.059 6003 Dihedral : 8.969 90.924 6093 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Rotamer: Outliers : 1.45 % Allowed : 9.42 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 4233 helix: 1.97 (0.20), residues: 705 sheet: 0.43 (0.14), residues: 1308 loop : -0.89 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 178 HIS 0.003 0.001 HIS F 188 PHE 0.020 0.001 PHE F 146 TYR 0.019 0.001 TYR B1067 ARG 0.011 0.000 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 227 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 146 PHE cc_start: 0.6919 (m-80) cc_final: 0.6551 (m-10) REVERT: H 225 LYS cc_start: 0.6766 (mppt) cc_final: 0.5454 (tptp) REVERT: B 233 ILE cc_start: 0.5851 (OUTLIER) cc_final: 0.5412 (pp) REVERT: F 225 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6930 (tppp) outliers start: 49 outliers final: 33 residues processed: 256 average time/residue: 1.3866 time to fit residues: 430.5221 Evaluate side-chains 254 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN H 221 ASN B 506 GLN B 703 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 34569 Z= 0.374 Angle : 0.695 12.653 47121 Z= 0.339 Chirality : 0.052 0.694 5592 Planarity : 0.005 0.063 6003 Dihedral : 9.388 113.613 6093 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.81 % Favored : 95.97 % Rotamer: Outliers : 1.47 % Allowed : 9.87 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.13), residues: 4233 helix: 1.70 (0.20), residues: 708 sheet: 0.31 (0.14), residues: 1350 loop : -0.94 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 178 HIS 0.005 0.001 HIS B 49 PHE 0.027 0.002 PHE C 906 TYR 0.020 0.002 TYR B1067 ARG 0.012 0.001 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 227 time to evaluate : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1145 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.7017 (tt) REVERT: L 44 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.7036 (ttm-80) REVERT: L 142 PHE cc_start: 0.4929 (m-10) cc_final: 0.4706 (m-80) REVERT: H 225 LYS cc_start: 0.6824 (mppt) cc_final: 0.5556 (tptp) REVERT: B 233 ILE cc_start: 0.5932 (OUTLIER) cc_final: 0.5556 (pp) REVERT: B 314 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: F 146 PHE cc_start: 0.6218 (m-10) cc_final: 0.5990 (m-80) REVERT: F 225 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6935 (tppp) outliers start: 50 outliers final: 28 residues processed: 257 average time/residue: 1.4072 time to fit residues: 436.7666 Evaluate side-chains 253 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 221 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 0.7980 chunk 393 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 382 optimal weight: 0.7980 chunk 230 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 345 optimal weight: 0.6980 chunk 361 optimal weight: 0.5980 chunk 381 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS C 134 GLN ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 HIS B 926 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN F 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34569 Z= 0.198 Angle : 0.626 12.171 47121 Z= 0.304 Chirality : 0.048 0.657 5592 Planarity : 0.004 0.060 6003 Dihedral : 8.875 98.718 6093 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Rotamer: Outliers : 1.20 % Allowed : 10.29 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 4233 helix: 1.93 (0.20), residues: 705 sheet: 0.40 (0.14), residues: 1299 loop : -0.91 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 178 HIS 0.004 0.001 HIS F 188 PHE 0.017 0.001 PHE B 133 TYR 0.018 0.001 TYR A1067 ARG 0.013 0.000 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 3.810 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8923 (mtp) cc_final: 0.8705 (mtp) REVERT: H 146 PHE cc_start: 0.7020 (m-10) cc_final: 0.6801 (m-10) REVERT: H 225 LYS cc_start: 0.6753 (mppt) cc_final: 0.5491 (tptt) REVERT: B 233 ILE cc_start: 0.5873 (OUTLIER) cc_final: 0.5486 (pp) REVERT: F 225 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.5706 (tptt) outliers start: 40 outliers final: 27 residues processed: 248 average time/residue: 1.4029 time to fit residues: 424.2009 Evaluate side-chains 247 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 0.6980 chunk 404 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 281 optimal weight: 0.0670 chunk 424 optimal weight: 20.0000 chunk 390 optimal weight: 0.9980 chunk 337 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 HIS B 134 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34569 Z= 0.188 Angle : 0.612 10.276 47121 Z= 0.296 Chirality : 0.048 0.639 5592 Planarity : 0.004 0.059 6003 Dihedral : 8.483 93.384 6093 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.34 % Favored : 96.45 % Rotamer: Outliers : 1.06 % Allowed : 10.54 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4233 helix: 1.99 (0.20), residues: 711 sheet: 0.40 (0.14), residues: 1311 loop : -0.86 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 178 HIS 0.003 0.001 HIS F 188 PHE 0.021 0.001 PHE D 146 TYR 0.036 0.001 TYR C 904 ARG 0.014 0.000 ARG G 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 223 time to evaluate : 3.716 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.8424 (ptm) cc_final: 0.8168 (ptp) REVERT: H 146 PHE cc_start: 0.6947 (m-10) cc_final: 0.6684 (m-10) REVERT: H 225 LYS cc_start: 0.6673 (mppt) cc_final: 0.5341 (tptt) REVERT: B 233 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5409 (pp) REVERT: B 314 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: F 225 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.5679 (tptt) outliers start: 35 outliers final: 27 residues processed: 245 average time/residue: 1.4317 time to fit residues: 423.8606 Evaluate side-chains 244 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.0000 chunk 360 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 338 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 347 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.094482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065106 restraints weight = 138550.014| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.13 r_work: 0.2791 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34569 Z= 0.251 Angle : 0.633 11.996 47121 Z= 0.308 Chirality : 0.048 0.645 5592 Planarity : 0.005 0.060 6003 Dihedral : 8.399 89.211 6093 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.28 % Rotamer: Outliers : 1.11 % Allowed : 10.54 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 4233 helix: 1.95 (0.20), residues: 705 sheet: 0.33 (0.14), residues: 1314 loop : -0.91 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 178 HIS 0.003 0.001 HIS F 188 PHE 0.022 0.002 PHE D 146 TYR 0.032 0.001 TYR C 904 ARG 0.013 0.000 ARG E 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9012.25 seconds wall clock time: 163 minutes 44.24 seconds (9824.24 seconds total)