Starting phenix.real_space_refine (version: dev) on Mon May 16 17:57:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/05_2022/7mw5_24063.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/05_2022/7mw5_24063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/05_2022/7mw5_24063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/05_2022/7mw5_24063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/05_2022/7mw5_24063.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw5_24063/05_2022/7mw5_24063.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 194": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 33635 Number of models: 1 Model: "" Number of chains: 41 Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1541 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 194, 'PCIS': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8149 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8140 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8140 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8320 Chain: "B" Number of atoms: 8145 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8315 Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1541 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 194, 'PCIS': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 8145 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8315 Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 843 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN C1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 Time building chain proxies: 28.05, per 1000 atoms: 0.83 Number of scatterers: 33635 At special positions: 0 Unit cell: (164.472, 163.404, 248.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 149 16.00 O 6626 8.00 N 5503 7.00 C 21357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 245 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 245 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 331 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 234 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 61 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 61 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 234 " " NAG I 1 " - " ASN C 282 " " NAG J 1 " - " ASN C 125 " " NAG K 1 " - " ASN C 331 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 343 " " NAG S 1 " - " ASN C 17 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 331 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B 717 " " NAG Z 1 " - " ASN B 709 " " NAG a 1 " - " ASN B 343 " " NAG b 1 " - " ASN B 17 " " NAG c 1 " - " ASN A 61 " " NAG d 1 " - " ASN A 282 " " NAG e 1 " - " ASN A 125 " " NAG f 1 " - " ASN A1134 " " NAG g 1 " - " ASN A1098 " " NAG h 1 " - " ASN A 801 " " NAG i 1 " - " ASN A 717 " " NAG j 1 " - " ASN A 709 " " NAG k 1 " - " ASN A 343 " " NAG l 1 " - " ASN A 17 " NAG-THR " NAG B1306 " - " THR B 124 " Time building additional restraints: 15.12 Conformation dependent library (CDL) restraints added in 8.0 seconds 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7912 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 77 sheets defined 18.9% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'L' and resid 50 through 54 Processing helix chain 'L' and resid 172 through 178 Processing helix chain 'L' and resid 234 through 239 Processing helix chain 'H' and resid 81 through 84 Processing helix chain 'H' and resid 237 through 242 removed outlier: 3.834A pdb=" N THR H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.927A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.511A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.784A pdb=" N LEU C 441 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C 442 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.528A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.364A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 941 removed outlier: 6.011A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.579A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.875A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.191A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.596A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.663A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.309A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 removed outlier: 3.715A pdb=" N TYR B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.093A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 921 through 941 removed outlier: 5.878A pdb=" N PHE B 927 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.755A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.537A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 172 through 179 removed outlier: 3.648A pdb=" N SER G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY G 179 " --> pdb=" O GLN G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 removed outlier: 4.107A pdb=" N HIS G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.908A pdb=" N GLY F 240 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.822A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.090A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.791A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.661A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.930A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.062A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 907 removed outlier: 3.610A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.353A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.600A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.548A pdb=" N THR E 54 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.570A pdb=" N PHE L 95 " --> pdb=" O CYS L 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'L' and resid 69 through 72 removed outlier: 6.509A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 69 through 72 removed outlier: 6.509A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 165 through 169 Processing sheet with id=AA6, first strand: chain 'L' and resid 205 through 206 removed outlier: 4.785A pdb=" N TRP L 199 " --> pdb=" O GLN L 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.566A pdb=" N CYS H 41 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA H 98 " --> pdb=" O CYS H 41 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR H 88 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.676A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.694A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.694A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 201 through 204 removed outlier: 4.512A pdb=" N TYR H 244 " --> pdb=" O VAL H 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.915A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.847A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.158A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.836A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 144 removed outlier: 6.080A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.466A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 325 through 326 removed outlier: 4.895A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.990A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.857A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.814A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 721 through 728 removed outlier: 7.078A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 721 through 728 Processing sheet with id=AC8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 790 removed outlier: 3.561A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AD2, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AD3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.917A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.070A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.601A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.114A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 196 through 197 Processing sheet with id=AD8, first strand: chain 'B' and resid 309 through 317 removed outlier: 6.599A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.741A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.569A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.388A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'B' and resid 721 through 728 removed outlier: 6.851A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.415A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.619A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 1080 through 1082 Processing sheet with id=AE9, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AF1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AF3, first strand: chain 'G' and resid 30 through 33 Processing sheet with id=AF4, first strand: chain 'G' and resid 69 through 70 Processing sheet with id=AF5, first strand: chain 'G' and resid 165 through 169 removed outlier: 3.847A pdb=" N SER G 165 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER G 182 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU G 232 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL G 184 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU G 230 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU G 186 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER G 228 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN G 188 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU G 226 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER G 225 " --> pdb=" O THR G 215 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 195 through 201 Processing sheet with id=AF7, first strand: chain 'F' and resid 24 through 26 removed outlier: 3.672A pdb=" N CYS F 41 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 98 " --> pdb=" O CYS F 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR F 99 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR F 90 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 101 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS F 86 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 77 through 79 removed outlier: 5.935A pdb=" N TRP F 66 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS F 57 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE F 70 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET F 53 " --> pdb=" O ILE F 70 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 170 through 174 removed outlier: 5.879A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 170 through 174 removed outlier: 5.879A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 201 through 204 Processing sheet with id=AG3, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.754A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.649A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.270A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AG7, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.746A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.278A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.009A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.571A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AH3, first strand: chain 'A' and resid 721 through 728 removed outlier: 6.827A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 721 through 728 Processing sheet with id=AH5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AH6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AH7, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AH8, first strand: chain 'A' and resid 1093 through 1097 Processing sheet with id=AH9, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AI1, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.574A pdb=" N GLU E 129 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.500A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AI4, first strand: chain 'D' and resid 77 through 79 removed outlier: 5.903A pdb=" N TRP D 66 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS D 57 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 70 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 53 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR D 127 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 87 through 92 1176 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.39 Time building geometry restraints manager: 16.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10570 1.34 - 1.46: 7950 1.46 - 1.58: 15670 1.58 - 1.70: 0 1.70 - 1.82: 194 Bond restraints: 34384 Sorted by residual: bond pdb=" C GLN B 173 " pdb=" N PRO B 174 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.35e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.426 1.508 -0.082 3.20e-02 9.77e+02 6.62e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.334 1.369 -0.035 1.51e-02 4.39e+03 5.32e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.426 1.494 -0.068 3.20e-02 9.77e+02 4.48e+00 bond pdb=" CA TYR C 674 " pdb=" C TYR C 674 " ideal model delta sigma weight residual 1.525 1.501 0.024 1.28e-02 6.10e+03 3.59e+00 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.18: 534 104.18 - 111.70: 16554 111.70 - 119.21: 11351 119.21 - 126.73: 17981 126.73 - 134.25: 404 Bond angle restraints: 46824 Sorted by residual: angle pdb=" C ALA B1070 " pdb=" N GLN B1071 " pdb=" CA GLN B1071 " ideal model delta sigma weight residual 121.33 128.42 -7.09 1.40e+00 5.10e-01 2.57e+01 angle pdb=" C LEU C 212 " pdb=" CA LEU C 212 " pdb=" CB LEU C 212 " ideal model delta sigma weight residual 115.79 110.12 5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" CA CYS H 115 " pdb=" CB CYS H 115 " pdb=" SG CYS H 115 " ideal model delta sigma weight residual 114.40 124.95 -10.55 2.30e+00 1.89e-01 2.11e+01 angle pdb=" N ALA B1070 " pdb=" CA ALA B1070 " pdb=" C ALA B1070 " ideal model delta sigma weight residual 107.32 114.80 -7.48 1.65e+00 3.67e-01 2.06e+01 angle pdb=" C LYS B1086 " pdb=" N ALA B1087 " pdb=" CA ALA B1087 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.70e+01 ... (remaining 46819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.44: 19018 22.44 - 44.87: 1056 44.87 - 67.31: 119 67.31 - 89.74: 69 89.74 - 112.18: 38 Dihedral angle restraints: 20300 sinusoidal: 7987 harmonic: 12313 Sorted by residual: dihedral pdb=" CA SER E 27 " pdb=" C SER E 27 " pdb=" N PRO E 28 " pdb=" CA PRO E 28 " ideal model delta harmonic sigma weight residual -180.00 -113.36 -66.64 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA SER G 27 " pdb=" C SER G 27 " pdb=" N PRO G 28 " pdb=" CA PRO G 28 " ideal model delta harmonic sigma weight residual -180.00 -114.49 -65.51 0 5.00e+00 4.00e-02 1.72e+02 dihedral pdb=" CA SER L 27 " pdb=" C SER L 27 " pdb=" N PRO L 28 " pdb=" CA PRO L 28 " ideal model delta harmonic sigma weight residual -180.00 -116.42 -63.58 0 5.00e+00 4.00e-02 1.62e+02 ... (remaining 20297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.255: 5559 0.255 - 0.510: 10 0.510 - 0.764: 3 0.764 - 1.019: 0 1.019 - 1.274: 1 Chirality restraints: 5573 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.45e+00 ... (remaining 5570 not shown) Planarity restraints: 5979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " 0.032 2.00e-02 2.50e+03 2.93e-02 1.07e+01 pdb=" CG ASN A 17 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS L 100 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO L 101 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO L 101 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 101 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 27 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C SER G 27 " -0.055 2.00e-02 2.50e+03 pdb=" O SER G 27 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO G 28 " 0.019 2.00e-02 2.50e+03 ... (remaining 5976 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 993 2.69 - 3.24: 33937 3.24 - 3.80: 53864 3.80 - 4.35: 71608 4.35 - 4.90: 115515 Nonbonded interactions: 275917 Sorted by model distance: nonbonded pdb=" OD2 ASP C 796 " pdb=" O6 NAG Z 1 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR G 60 " pdb=" O ARG F 119 " model vdw 2.166 2.440 nonbonded pdb=" NE2 GLN D 25 " pdb=" O TYR D 113 " model vdw 2.168 2.520 nonbonded pdb=" ND2 ASN F 54 " pdb=" O SER F 118 " model vdw 2.169 2.520 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.178 2.440 ... (remaining 275912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1308)) selection = (chain 'B' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1308)) selection = (chain 'C' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1145 or resid 1301 through 1308)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 149 5.16 5 C 21357 2.51 5 N 5503 2.21 5 O 6626 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.730 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: 0.030 Extract box with map and model: 14.050 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.280 Process input model: 101.070 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.003 0.082 34384 Z= 0.216 Angle : 0.685 10.555 46824 Z= 0.385 Chirality : 0.052 1.274 5573 Planarity : 0.005 0.082 5929 Dihedral : 15.225 112.178 12244 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.96 % Favored : 91.47 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 4193 helix: 0.78 (0.20), residues: 670 sheet: -0.95 (0.16), residues: 1064 loop : -1.99 (0.12), residues: 2459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.4333 time to fit residues: 164.7055 Evaluate side-chains 157 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.916 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 176 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 328 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 199 optimal weight: 0.2980 chunk 244 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 HIS L 175 GLN ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS H 247 ASN H 249 ASN C 69 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN B 641 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN G 211 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 901 GLN E 26 GLN E 100 HIS ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.127 34384 Z= 0.268 Angle : 0.654 13.347 46824 Z= 0.351 Chirality : 0.053 1.305 5573 Planarity : 0.006 0.122 5929 Dihedral : 12.986 111.664 5019 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.46 % Favored : 90.99 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 4193 helix: 1.15 (0.20), residues: 668 sheet: -0.89 (0.16), residues: 1091 loop : -1.97 (0.12), residues: 2434 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 186 average time/residue: 0.4306 time to fit residues: 137.4467 Evaluate side-chains 164 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 4.123 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3344 time to fit residues: 14.5389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 316 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 381 optimal weight: 3.9990 chunk 411 optimal weight: 5.9990 chunk 339 optimal weight: 7.9990 chunk 378 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN G 58 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 34384 Z= 0.209 Angle : 0.616 15.997 46824 Z= 0.328 Chirality : 0.051 1.193 5573 Planarity : 0.005 0.130 5929 Dihedral : 12.916 111.664 5019 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.05 % Favored : 91.44 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 4193 helix: 1.35 (0.20), residues: 674 sheet: -0.86 (0.16), residues: 1078 loop : -1.91 (0.12), residues: 2441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 5.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 184 average time/residue: 0.4920 time to fit residues: 160.7604 Evaluate side-chains 157 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 4.095 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3472 time to fit residues: 8.5707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 181 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 382 optimal weight: 2.9990 chunk 405 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 362 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN C 69 HIS C 388 ASN C 954 GLN B 641 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.126 34384 Z= 0.252 Angle : 0.619 14.564 46824 Z= 0.330 Chirality : 0.052 1.191 5573 Planarity : 0.005 0.130 5929 Dihedral : 12.903 111.554 5019 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.68 % Favored : 90.92 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 4193 helix: 1.38 (0.20), residues: 673 sheet: -0.86 (0.16), residues: 1072 loop : -1.88 (0.12), residues: 2448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 3.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 167 average time/residue: 0.4325 time to fit residues: 125.7565 Evaluate side-chains 153 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 3.920 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3191 time to fit residues: 9.3201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 301 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 954 GLN B 641 ASN B1005 GLN G 211 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.136 34384 Z= 0.416 Angle : 0.703 15.260 46824 Z= 0.374 Chirality : 0.055 1.256 5573 Planarity : 0.006 0.134 5929 Dihedral : 13.030 111.591 5019 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.94 % Favored : 89.63 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 4193 helix: 1.08 (0.20), residues: 667 sheet: -1.00 (0.16), residues: 1065 loop : -1.98 (0.12), residues: 2461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 175 average time/residue: 0.4339 time to fit residues: 132.0971 Evaluate side-chains 155 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 3.883 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.3183 time to fit residues: 11.9551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 2.9990 chunk 364 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 405 optimal weight: 7.9990 chunk 336 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 33 optimal weight: 0.0870 chunk 134 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN G 211 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 34384 Z= 0.201 Angle : 0.606 14.442 46824 Z= 0.322 Chirality : 0.051 1.131 5573 Planarity : 0.005 0.137 5929 Dihedral : 12.910 111.687 5019 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.27 % Favored : 91.37 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 4193 helix: 1.42 (0.20), residues: 665 sheet: -0.97 (0.15), residues: 1116 loop : -1.83 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 181 average time/residue: 0.4461 time to fit residues: 138.8826 Evaluate side-chains 160 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 3.733 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2933 time to fit residues: 10.2498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 390 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 230 optimal weight: 0.7980 chunk 296 optimal weight: 4.9990 chunk 229 optimal weight: 0.5980 chunk 341 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 403 optimal weight: 20.0000 chunk 252 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 HIS ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.144 34384 Z= 0.206 Angle : 0.602 14.510 46824 Z= 0.321 Chirality : 0.050 1.101 5573 Planarity : 0.005 0.152 5929 Dihedral : 12.857 111.606 5019 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.63 % Favored : 91.01 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 4193 helix: 1.58 (0.20), residues: 664 sheet: -0.89 (0.15), residues: 1109 loop : -1.79 (0.12), residues: 2420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 170 average time/residue: 0.4542 time to fit residues: 133.0009 Evaluate side-chains 149 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 4.094 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3775 time to fit residues: 9.1296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 249 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 317 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN B 641 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.163 34384 Z= 0.205 Angle : 0.605 14.449 46824 Z= 0.324 Chirality : 0.050 1.067 5573 Planarity : 0.006 0.155 5929 Dihedral : 12.834 111.572 5019 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.51 % Favored : 91.16 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4193 helix: 1.66 (0.20), residues: 661 sheet: -0.84 (0.16), residues: 1088 loop : -1.75 (0.12), residues: 2444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 172 average time/residue: 0.4293 time to fit residues: 127.8369 Evaluate side-chains 155 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 3.825 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.3026 time to fit residues: 9.0819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 367 optimal weight: 0.7980 chunk 386 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 376 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 295 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 340 optimal weight: 0.9990 chunk 355 optimal weight: 5.9990 chunk 375 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.129 34384 Z= 0.247 Angle : 0.615 13.456 46824 Z= 0.327 Chirality : 0.051 1.082 5573 Planarity : 0.006 0.171 5929 Dihedral : 12.841 111.750 5019 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.01 % Favored : 90.63 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 4193 helix: 1.63 (0.20), residues: 660 sheet: -0.81 (0.16), residues: 1039 loop : -1.76 (0.12), residues: 2494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 4.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 160 average time/residue: 0.4306 time to fit residues: 121.8818 Evaluate side-chains 150 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 4.392 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3544 time to fit residues: 8.7945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 247 optimal weight: 0.3980 chunk 397 optimal weight: 20.0000 chunk 242 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 276 optimal weight: 6.9990 chunk 417 optimal weight: 2.9990 chunk 384 optimal weight: 0.0970 chunk 332 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 203 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 34384 Z= 0.199 Angle : 0.596 15.688 46824 Z= 0.317 Chirality : 0.050 1.046 5573 Planarity : 0.006 0.179 5929 Dihedral : 12.808 111.571 5019 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.37 % Favored : 91.25 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 4193 helix: 1.73 (0.20), residues: 659 sheet: -0.77 (0.16), residues: 1058 loop : -1.71 (0.12), residues: 2476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 164 average time/residue: 0.4405 time to fit residues: 126.4868 Evaluate side-chains 153 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 3.953 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3073 time to fit residues: 6.4755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 264 optimal weight: 6.9990 chunk 354 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 341 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 66 GLN ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.079307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057313 restraints weight = 293443.713| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.92 r_work: 0.3177 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work: 0.3134 rms_B_bonded: 4.52 restraints_weight: 0.1250 r_work: 0.3109 rms_B_bonded: 4.67 restraints_weight: 0.0625 r_work: 0.3082 rms_B_bonded: 4.94 restraints_weight: 0.0312 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.379 34384 Z= 0.463 Angle : 0.725 19.177 46824 Z= 0.389 Chirality : 0.055 1.175 5573 Planarity : 0.006 0.182 5929 Dihedral : 12.989 112.254 5019 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.01 % Favored : 89.60 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 4193 helix: 1.21 (0.20), residues: 667 sheet: -0.99 (0.16), residues: 1038 loop : -1.86 (0.12), residues: 2488 =============================================================================== Job complete usr+sys time: 5215.30 seconds wall clock time: 98 minutes 8.33 seconds (5888.33 seconds total)