Starting phenix.real_space_refine on Mon Feb 19 23:50:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoj_26648/02_2024/7uoj_26648.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoj_26648/02_2024/7uoj_26648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoj_26648/02_2024/7uoj_26648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoj_26648/02_2024/7uoj_26648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoj_26648/02_2024/7uoj_26648.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoj_26648/02_2024/7uoj_26648.pdb" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 16356 2.51 5 N 4368 2.21 5 O 5259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 140": "OD1" <-> "OD2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "l TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 53": "OD1" <-> "OD2" Residue "l GLU 79": "OE1" <-> "OE2" Residue "l ASP 92": "OD1" <-> "OD2" Residue "h TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "J GLU 634": "OE1" <-> "OE2" Residue "J GLU 647": "OE1" <-> "OE2" Residue "K ASP 76": "OD1" <-> "OD2" Residue "K ASP 76": "OD1" <-> "OD2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "m ASP 92": "OD1" <-> "OD2" Residue "k GLU 6": "OE1" <-> "OE2" Residue "k ASP 86": "OD1" <-> "OD2" Residue "k PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26133 Number of models: 1 Model: "" Number of chains: 54 Chain: "G" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "B" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "L" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "l" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "h" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "C" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "E" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "e" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "d" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "I" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "m" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "k" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 13.20, per 1000 atoms: 0.51 Number of scatterers: 26133 At special positions: 0 Unit cell: (159.796, 161.186, 155.628, 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 150 16.00 O 5259 8.00 N 4368 7.00 C 16356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.05 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 88 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.05 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 88 " distance=2.03 Simple disulfide: pdb=" SG CYS k 22 " - pdb=" SG CYS k 92 " 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 ALPHA1-2 " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 8 " " BMA q 3 " - " MAN q 4 " " BMA u 3 " - " MAN u 4 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 9 " " BMA u 3 " - " MAN u 5 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 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 q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 339 " " NAG F 1 " - " ASN G 156 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 339 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 197 " " NAG I 604 " - " ASN I 234 " " NAG I 605 " - " ASN I 339 " " NAG N 1 " - " ASN G 160 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 295 " " NAG Q 1 " - " ASN G 301 " " NAG R 1 " - " ASN G 363 " " NAG S 1 " - " ASN G 386 " " NAG T 1 " - " ASN G 392 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 448 " " NAG X 1 " - " ASN A 156 " " NAG Y 1 " - " ASN A 160 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 301 " " NAG c 1 " - " ASN A 363 " " NAG f 1 " - " ASN A 386 " " NAG g 1 " - " ASN A 392 " " NAG i 1 " - " ASN A 332 " " NAG j 1 " - " ASN A 448 " " NAG o 1 " - " ASN I 156 " " NAG p 1 " - " ASN I 160 " " NAG q 1 " - " ASN I 262 " " NAG r 1 " - " ASN I 295 " " NAG s 1 " - " ASN I 301 " " NAG t 1 " - " ASN I 363 " " NAG u 1 " - " ASN I 386 " " NAG v 1 " - " ASN I 392 " " NAG w 1 " - " ASN I 332 " " NAG x 1 " - " ASN I 448 " Time building additional restraints: 11.07 Conformation dependent library (CDL) restraints added in 5.2 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 62 sheets defined 15.7% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.673A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 115 removed outlier: 3.507A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 4.134A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 334 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.865A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.973A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 4.053A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 521 Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.106A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 571 through 595 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.242A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 664 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.692A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 25 through 31 removed outlier: 4.503A pdb=" N HIS L 30 " --> pdb=" O GLY L 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 79 through 83 removed outlier: 4.087A pdb=" N GLU l 83 " --> pdb=" O ALA l 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 87 removed outlier: 3.948A pdb=" N ASP h 86 " --> pdb=" O THR h 83 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER h 87 " --> pdb=" O ALA h 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 83 through 87' Processing helix chain 'h' and resid 100D through 100H Processing helix chain 'A' and resid 57 through 63 removed outlier: 4.159A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.786A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.365A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.922A pdb=" N GLY A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.037A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.865A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 571 through 595 Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.565A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 664 Processing helix chain 'E' and resid 25 through 31 removed outlier: 4.433A pdb=" N HIS E 30 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 83 removed outlier: 4.096A pdb=" N GLU e 83 " --> pdb=" O ALA e 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 100D through 100H removed outlier: 3.599A pdb=" N ASN d 100H" --> pdb=" O VAL d 100E" (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 removed outlier: 3.590A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 114 Processing helix chain 'I' and resid 115 through 117 No H-bonds generated for 'chain 'I' and resid 115 through 117' Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.988A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 181 No H-bonds generated for 'chain 'I' and resid 179 through 181' Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.915A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.965A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.008A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 520 removed outlier: 4.542A pdb=" N VAL J 518 " --> pdb=" O GLY J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 536 removed outlier: 3.635A pdb=" N THR J 536 " --> pdb=" O ALA J 532 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 543 through 545 No H-bonds generated for 'chain 'J' and resid 543 through 545' Processing helix chain 'J' and resid 571 through 595 Processing helix chain 'J' and resid 627 through 638 removed outlier: 4.571A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER J 636 " --> pdb=" O ASP J 632 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN J 637 " --> pdb=" O LYS J 633 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 664 Processing helix chain 'M' and resid 25 through 31 removed outlier: 4.483A pdb=" N HIS M 30 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 83 removed outlier: 4.120A pdb=" N GLU m 83 " --> pdb=" O ALA m 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'G' and resid 495 through 499 removed outlier: 4.982A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.720A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 244 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 84 " --> pdb=" O THR G 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.296A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 93 removed outlier: 4.057A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'G' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 201 through 203 removed outlier: 3.515A pdb=" N TYR G 435 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 271 through 273 removed outlier: 4.119A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 4.119A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.372A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.549A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 359 through 360 removed outlier: 3.603A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.526A pdb=" N GLY H 76G" --> pdb=" O VAL H 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.368A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 13 removed outlier: 3.595A pdb=" N THR L 105 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB7, first strand: chain 'l' and resid 9 through 13 removed outlier: 6.059A pdb=" N ILE l 9 " --> pdb=" O THR l 103 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR l 105 " --> pdb=" O ILE l 9 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP l 35 " --> pdb=" O ILE l 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 19 through 22 Processing sheet with id=AB9, first strand: chain 'h' and resid 4 through 7 removed outlier: 4.082A pdb=" N GLN h 77 " --> pdb=" O ASP h 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP h 72 " --> pdb=" O GLN h 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 58 through 59 removed outlier: 7.067A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 100 through 100A removed outlier: 4.009A pdb=" N ARG h 100 " --> pdb=" O PHE h 100K" (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE h 100K" --> pdb=" O ARG h 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.040A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.820A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.439A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.055A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 169 through 177 removed outlier: 4.248A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.511A pdb=" N TYR A 435 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.075A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.075A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.146A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.656A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AD4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.969A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 8 through 13 removed outlier: 6.215A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AD8, first strand: chain 'e' and resid 9 through 13 removed outlier: 5.995A pdb=" N ILE e 9 " --> pdb=" O THR e 103 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR e 105 " --> pdb=" O ILE e 9 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE e 11 " --> pdb=" O THR e 105 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLN e 37 " --> pdb=" O LEU e 46 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU e 46 " --> pdb=" O GLN e 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 19 through 22 Processing sheet with id=AE1, first strand: chain 'd' and resid 4 through 7 removed outlier: 4.572A pdb=" N GLN d 77 " --> pdb=" O ASP d 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP d 72 " --> pdb=" O GLN d 77 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 57 through 59 removed outlier: 7.002A pdb=" N TRP d 36 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR d 50 " --> pdb=" O TRP d 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP d 34 " --> pdb=" O TYR d 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 100 through 100A removed outlier: 3.902A pdb=" N ARG d 100 " --> pdb=" O PHE d 100K" (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE d 100K" --> pdb=" O ARG d 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'I' and resid 495 through 499 removed outlier: 5.025A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.717A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR I 244 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE I 84 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 75 through 76 removed outlier: 4.324A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.094A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 130 through 133 Processing sheet with id=AE9, first strand: chain 'I' and resid 182 through 183 Processing sheet with id=AF1, first strand: chain 'I' and resid 201 through 203 Processing sheet with id=AF2, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.895A pdb=" N LEU I 285 " --> pdb=" O ARG I 273 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.895A pdb=" N LEU I 285 " --> pdb=" O ARG I 273 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.853A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.268A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AF5, first strand: chain 'I' and resid 359 through 360 removed outlier: 3.795A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 375 through 377 removed outlier: 4.640A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.693A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 8 through 13 removed outlier: 3.757A pdb=" N THR M 105 " --> pdb=" O MET M 11 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AG2, first strand: chain 'm' and resid 9 through 13 removed outlier: 6.067A pdb=" N ILE m 9 " --> pdb=" O THR m 103 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR m 105 " --> pdb=" O ILE m 9 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE m 11 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN m 37 " --> pdb=" O LEU m 46 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU m 46 " --> pdb=" O GLN m 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 19 through 22 Processing sheet with id=AG4, first strand: chain 'm' and resid 31 through 32 Processing sheet with id=AG5, first strand: chain 'k' and resid 4 through 7 removed outlier: 4.218A pdb=" N GLN k 77 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP k 72 " --> pdb=" O GLN k 77 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 58 through 59 removed outlier: 6.984A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL k 100R" --> pdb=" O ARG k 94 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU k 96 " --> pdb=" O MET k 100P" (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET k 100P" --> pdb=" O LEU k 96 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 58 through 59 removed outlier: 6.984A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'k' and resid 100 through 100A removed outlier: 3.835A pdb=" N ARG k 100 " --> pdb=" O PHE k 100K" (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE k 100K" --> pdb=" O ARG k 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 825 hydrogen bonds defined for protein. 2106 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: 9.79 Time building geometry restraints manager: 11.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8193 1.34 - 1.47: 7177 1.47 - 1.61: 11119 1.61 - 1.74: 4 1.74 - 1.88: 207 Bond restraints: 26700 Sorted by residual: bond pdb=" C1 MAN w 9 " pdb=" C2 MAN w 9 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C CYS A 385 " pdb=" N ASN A 386 " ideal model delta sigma weight residual 1.328 1.383 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" N VAL A 208 " pdb=" CA VAL A 208 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.91e+00 bond pdb=" N ILE B 603 " pdb=" CA ILE B 603 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.80e+00 bond pdb=" CB CYS G 296 " pdb=" SG CYS G 296 " ideal model delta sigma weight residual 1.808 1.717 0.091 3.30e-02 9.18e+02 7.67e+00 ... (remaining 26695 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.09: 479 105.09 - 112.39: 14405 112.39 - 119.68: 8648 119.68 - 126.97: 12334 126.97 - 134.26: 416 Bond angle restraints: 36282 Sorted by residual: angle pdb=" N VAL I 371 " pdb=" CA VAL I 371 " pdb=" C VAL I 371 " ideal model delta sigma weight residual 113.71 107.35 6.36 9.50e-01 1.11e+00 4.48e+01 angle pdb=" CA CYS G 296 " pdb=" CB CYS G 296 " pdb=" SG CYS G 296 " ideal model delta sigma weight residual 114.40 128.92 -14.52 2.30e+00 1.89e-01 3.99e+01 angle pdb=" CA CYS I 296 " pdb=" CB CYS I 296 " pdb=" SG CYS I 296 " ideal model delta sigma weight residual 114.40 128.49 -14.09 2.30e+00 1.89e-01 3.75e+01 angle pdb=" C CYS A 385 " pdb=" N ASN A 386 " pdb=" CA ASN A 386 " ideal model delta sigma weight residual 122.67 112.42 10.25 1.73e+00 3.34e-01 3.51e+01 angle pdb=" C CYS G 385 " pdb=" N ASN G 386 " pdb=" CA ASN G 386 " ideal model delta sigma weight residual 122.03 110.26 11.77 2.01e+00 2.48e-01 3.43e+01 ... (remaining 36277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.79: 16048 24.79 - 49.59: 962 49.59 - 74.38: 206 74.38 - 99.17: 109 99.17 - 123.97: 90 Dihedral angle restraints: 17415 sinusoidal: 8421 harmonic: 8994 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 160.33 -67.33 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual 93.00 34.75 58.25 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS I 296 " pdb=" SG CYS I 296 " pdb=" SG CYS I 331 " pdb=" CB CYS I 331 " ideal model delta sinusoidal sigma weight residual 93.00 39.60 53.40 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 17412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 4324 0.198 - 0.397: 25 0.397 - 0.595: 1 0.595 - 0.794: 1 0.794 - 0.992: 2 Chirality restraints: 4353 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN G 386 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C1 NAG u 1 " pdb=" ND2 ASN I 386 " pdb=" C2 NAG u 1 " pdb=" O5 NAG u 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 4350 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 386 " -0.005 2.00e-02 2.50e+03 7.95e-02 7.89e+01 pdb=" CG ASN G 386 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN G 386 " -0.095 2.00e-02 2.50e+03 pdb=" ND2 ASN G 386 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 386 " -0.000 2.00e-02 2.50e+03 5.46e-02 3.73e+01 pdb=" CG ASN I 386 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN I 386 " 0.066 2.00e-02 2.50e+03 pdb=" ND2 ASN I 386 " -0.055 2.00e-02 2.50e+03 pdb=" C1 NAG u 1 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 386 " -0.000 2.00e-02 2.50e+03 4.85e-02 2.94e+01 pdb=" CG ASN A 386 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 386 " 0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN A 386 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " 0.050 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2452 2.74 - 3.28: 25476 3.28 - 3.82: 40243 3.82 - 4.36: 44846 4.36 - 4.90: 78279 Nonbonded interactions: 191296 Sorted by model distance: nonbonded pdb=" NH1 ARG G 298 " pdb=" OD1 ASN G 302 " model vdw 2.198 2.520 nonbonded pdb=" O GLN k 3 " pdb=" OG SER k 25 " model vdw 2.198 2.440 nonbonded pdb=" OG SER l 30 " pdb=" OG SER l 93 " model vdw 2.202 2.440 nonbonded pdb=" OG SER m 65 " pdb=" OG1 THR m 72 " model vdw 2.203 2.440 nonbonded pdb=" NH1 ARG A 298 " pdb=" OD1 ASN A 302 " model vdw 2.206 2.520 ... (remaining 191291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'g' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'O' selection = chain 'Z' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'c' selection = chain 't' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 'u' } ncs_group { reference = chain 'U' selection = chain 'i' selection = chain 'w' } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.140 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 69.320 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.006 0.091 26700 Z= 0.407 Angle : 0.863 14.524 36282 Z= 0.419 Chirality : 0.058 0.992 4353 Planarity : 0.005 0.128 4482 Dihedral : 19.284 123.966 11514 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.93 % Favored : 90.74 % Rotamer: Outliers : 0.11 % Allowed : 0.63 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 3090 helix: 0.71 (0.31), residues: 325 sheet: -0.70 (0.17), residues: 888 loop : -1.87 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 112 HIS 0.011 0.001 HIS h 97 PHE 0.031 0.002 PHE I 288 TYR 0.019 0.002 TYR H 91 ARG 0.009 0.001 ARG l 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 454 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 622 ILE cc_start: 0.8044 (tp) cc_final: 0.7815 (tp) REVERT: B 626 MET cc_start: 0.7067 (pmm) cc_final: 0.6566 (pmm) REVERT: L 87 ILE cc_start: 0.7214 (mt) cc_final: 0.6880 (mt) REVERT: l 62 PHE cc_start: 0.7020 (m-80) cc_final: 0.6696 (m-80) REVERT: A 119 CYS cc_start: 0.5519 (m) cc_final: 0.5239 (m) REVERT: C 626 MET cc_start: 0.6970 (pmm) cc_final: 0.6479 (pmm) REVERT: C 630 GLN cc_start: 0.7707 (mt0) cc_final: 0.7232 (pp30) REVERT: D 31 ASP cc_start: 0.6770 (p0) cc_final: 0.6561 (p0) REVERT: e 37 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7600 (tm-30) REVERT: e 61 ARG cc_start: 0.6198 (mtm180) cc_final: 0.5730 (mtm-85) REVERT: d 2 MET cc_start: 0.6101 (pmm) cc_final: 0.5799 (pmm) REVERT: I 207 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7571 (mtmm) REVERT: J 603 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7447 (tp) REVERT: J 622 ILE cc_start: 0.7971 (tp) cc_final: 0.7580 (tp) REVERT: J 626 MET cc_start: 0.6811 (pmm) cc_final: 0.6413 (pmm) REVERT: K 85 ASP cc_start: 0.6385 (p0) cc_final: 0.5816 (p0) outliers start: 3 outliers final: 0 residues processed: 457 average time/residue: 0.3337 time to fit residues: 246.4736 Evaluate side-chains 359 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 357 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 277 optimal weight: 0.0270 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN h 52 HIS h 97 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 77 ASN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 34 GLN m 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26700 Z= 0.212 Angle : 0.658 13.086 36282 Z= 0.319 Chirality : 0.048 0.489 4353 Planarity : 0.004 0.081 4482 Dihedral : 16.702 110.378 5823 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.06 % Favored : 92.72 % Rotamer: Outliers : 0.22 % Allowed : 5.40 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 3090 helix: 0.93 (0.30), residues: 330 sheet: -0.61 (0.17), residues: 861 loop : -1.74 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 112 HIS 0.008 0.001 HIS h 97 PHE 0.020 0.002 PHE G 288 TYR 0.014 0.001 TYR I 435 ARG 0.008 0.000 ARG m 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 451 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8601 (tp) cc_final: 0.8110 (pt) REVERT: L 87 ILE cc_start: 0.7338 (mt) cc_final: 0.6974 (mt) REVERT: l 54 ARG cc_start: 0.7481 (ptm-80) cc_final: 0.6868 (ptt90) REVERT: l 92 ASP cc_start: 0.7815 (p0) cc_final: 0.7544 (p0) REVERT: A 119 CYS cc_start: 0.5956 (m) cc_final: 0.5542 (m) REVERT: A 376 PHE cc_start: 0.8504 (p90) cc_final: 0.8290 (p90) REVERT: C 622 ILE cc_start: 0.7790 (tp) cc_final: 0.7452 (tp) REVERT: C 626 MET cc_start: 0.6930 (pmm) cc_final: 0.6703 (pmm) REVERT: D 31 ASP cc_start: 0.6619 (p0) cc_final: 0.6400 (p0) REVERT: e 60 GLU cc_start: 0.7057 (pp20) cc_final: 0.6787 (pp20) REVERT: e 61 ARG cc_start: 0.7118 (mtm180) cc_final: 0.6838 (mtm-85) REVERT: e 62 PHE cc_start: 0.7474 (m-80) cc_final: 0.7139 (m-80) REVERT: d 2 MET cc_start: 0.6136 (pmm) cc_final: 0.5906 (pmm) REVERT: J 622 ILE cc_start: 0.7940 (tp) cc_final: 0.7390 (tp) REVERT: J 626 MET cc_start: 0.6708 (pmm) cc_final: 0.6435 (pmm) REVERT: K 85 ASP cc_start: 0.6296 (p0) cc_final: 0.5729 (p0) outliers start: 6 outliers final: 1 residues processed: 454 average time/residue: 0.3352 time to fit residues: 248.3593 Evaluate side-chains 375 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 278 optimal weight: 0.0170 chunk 300 optimal weight: 20.0000 chunk 247 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 overall best weight: 2.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN G 425 ASN G 478 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN D 39 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 26700 Z= 0.358 Angle : 0.738 13.490 36282 Z= 0.359 Chirality : 0.050 0.456 4353 Planarity : 0.005 0.063 4482 Dihedral : 15.507 114.249 5823 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.06 % Favored : 90.71 % Rotamer: Outliers : 0.22 % Allowed : 5.62 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.15), residues: 3090 helix: 0.82 (0.30), residues: 330 sheet: -0.79 (0.16), residues: 897 loop : -1.89 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP l 35 HIS 0.010 0.001 HIS I 374 PHE 0.031 0.002 PHE I 288 TYR 0.019 0.002 TYR H 91 ARG 0.006 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 450 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 TRP cc_start: 0.8412 (t-100) cc_final: 0.8170 (t-100) REVERT: G 201 ILE cc_start: 0.8561 (tp) cc_final: 0.8117 (pt) REVERT: G 427 TRP cc_start: 0.7244 (m-90) cc_final: 0.6836 (m-90) REVERT: B 622 ILE cc_start: 0.8145 (tp) cc_final: 0.7923 (tp) REVERT: B 626 MET cc_start: 0.7120 (pmm) cc_final: 0.6905 (pmm) REVERT: H 85 ASP cc_start: 0.6219 (p0) cc_final: 0.5936 (p0) REVERT: L 87 ILE cc_start: 0.7197 (mt) cc_final: 0.6931 (mt) REVERT: l 54 ARG cc_start: 0.7890 (ptm-80) cc_final: 0.7551 (ptt90) REVERT: h 53 LYS cc_start: 0.7476 (mmmm) cc_final: 0.7226 (mmmm) REVERT: A 119 CYS cc_start: 0.6223 (m) cc_final: 0.5920 (m) REVERT: A 376 PHE cc_start: 0.8635 (p90) cc_final: 0.8264 (p90) REVERT: A 395 TRP cc_start: 0.7454 (m-10) cc_final: 0.7003 (m-10) REVERT: A 434 MET cc_start: 0.8556 (ptp) cc_final: 0.8342 (ptm) REVERT: C 622 ILE cc_start: 0.7779 (tp) cc_final: 0.7552 (tp) REVERT: D 31 ASP cc_start: 0.6917 (p0) cc_final: 0.6664 (p0) REVERT: D 76 ASP cc_start: 0.7334 (p0) cc_final: 0.7110 (p0) REVERT: e 37 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7570 (tm-30) REVERT: e 60 GLU cc_start: 0.7229 (pp20) cc_final: 0.6702 (pp20) REVERT: e 61 ARG cc_start: 0.7213 (mtm180) cc_final: 0.6944 (mtm-85) REVERT: I 112 TRP cc_start: 0.8442 (t-100) cc_final: 0.8140 (t-100) REVERT: J 622 ILE cc_start: 0.7934 (tp) cc_final: 0.7407 (tp) REVERT: J 626 MET cc_start: 0.6400 (pmm) cc_final: 0.6173 (pmm) REVERT: K 85 ASP cc_start: 0.6402 (p0) cc_final: 0.5821 (p0) REVERT: M 79 GLN cc_start: 0.7124 (tm-30) cc_final: 0.6076 (tm-30) REVERT: m 62 PHE cc_start: 0.6649 (m-80) cc_final: 0.6019 (m-80) REVERT: k 52 HIS cc_start: 0.5217 (t-90) cc_final: 0.4990 (t-90) outliers start: 6 outliers final: 4 residues processed: 456 average time/residue: 0.3419 time to fit residues: 254.1907 Evaluate side-chains 381 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 377 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.0060 chunk 209 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 186 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 77 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 26700 Z= 0.217 Angle : 0.669 12.991 36282 Z= 0.321 Chirality : 0.048 0.474 4353 Planarity : 0.004 0.053 4482 Dihedral : 14.290 109.676 5823 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.02 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 3090 helix: 1.02 (0.30), residues: 318 sheet: -0.69 (0.17), residues: 861 loop : -1.73 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP e 35 HIS 0.005 0.001 HIS I 374 PHE 0.017 0.002 PHE G 288 TYR 0.013 0.001 TYR J 638 ARG 0.006 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 TRP cc_start: 0.8339 (t-100) cc_final: 0.8086 (t-100) REVERT: G 201 ILE cc_start: 0.8519 (tp) cc_final: 0.8123 (pt) REVERT: G 427 TRP cc_start: 0.7066 (m-90) cc_final: 0.6717 (m-90) REVERT: B 626 MET cc_start: 0.7194 (pmm) cc_final: 0.6935 (pmm) REVERT: H 85 ASP cc_start: 0.6260 (p0) cc_final: 0.5916 (p0) REVERT: L 87 ILE cc_start: 0.7154 (mt) cc_final: 0.6855 (mt) REVERT: l 54 ARG cc_start: 0.7838 (ptm-80) cc_final: 0.7519 (ptt90) REVERT: h 53 LYS cc_start: 0.7679 (mmmm) cc_final: 0.7306 (mmmm) REVERT: A 119 CYS cc_start: 0.6156 (m) cc_final: 0.5917 (m) REVERT: A 376 PHE cc_start: 0.8714 (p90) cc_final: 0.8348 (p90) REVERT: C 630 GLN cc_start: 0.7371 (mt0) cc_final: 0.6821 (mt0) REVERT: D 31 ASP cc_start: 0.6913 (p0) cc_final: 0.6458 (p0) REVERT: D 76 ASP cc_start: 0.7263 (p0) cc_final: 0.7050 (p0) REVERT: e 60 GLU cc_start: 0.7198 (pp20) cc_final: 0.6699 (pp20) REVERT: e 61 ARG cc_start: 0.7373 (mtm180) cc_final: 0.7168 (mtm-85) REVERT: d 2 MET cc_start: 0.6247 (pmm) cc_final: 0.5894 (pmm) REVERT: d 94 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6732 (mmm-85) REVERT: J 622 ILE cc_start: 0.7921 (tp) cc_final: 0.7419 (tp) REVERT: K 85 ASP cc_start: 0.6519 (p0) cc_final: 0.5909 (p0) REVERT: M 79 GLN cc_start: 0.7391 (tm-30) cc_final: 0.6314 (tm-30) REVERT: m 62 PHE cc_start: 0.6339 (m-80) cc_final: 0.5797 (m-80) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.3450 time to fit residues: 262.3588 Evaluate side-chains 383 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.5980 chunk 167 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 220 optimal weight: 0.1980 chunk 122 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 652 GLN H 39 GLN L 77 ASN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN D 39 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN m 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 26700 Z= 0.404 Angle : 0.784 13.559 36282 Z= 0.383 Chirality : 0.051 0.450 4353 Planarity : 0.005 0.060 4482 Dihedral : 13.902 114.613 5823 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.87 % Favored : 89.90 % Rotamer: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3090 helix: 0.64 (0.29), residues: 329 sheet: -0.92 (0.16), residues: 894 loop : -1.96 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP l 35 HIS 0.009 0.002 HIS I 374 PHE 0.031 0.003 PHE G 288 TYR 0.023 0.002 TYR H 91 ARG 0.006 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 457 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8584 (tp) cc_final: 0.8203 (pt) REVERT: G 369 LEU cc_start: 0.8948 (tp) cc_final: 0.8602 (tt) REVERT: H 85 ASP cc_start: 0.6488 (p0) cc_final: 0.6127 (p0) REVERT: L 87 ILE cc_start: 0.7124 (mt) cc_final: 0.6844 (mt) REVERT: h 2 MET cc_start: 0.5158 (tpp) cc_final: 0.4890 (tpp) REVERT: h 53 LYS cc_start: 0.8004 (mmmm) cc_final: 0.7493 (mtpt) REVERT: D 31 ASP cc_start: 0.6993 (p0) cc_final: 0.6764 (p0) REVERT: e 37 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7440 (tm-30) REVERT: J 622 ILE cc_start: 0.8126 (tp) cc_final: 0.7641 (tp) REVERT: J 626 MET cc_start: 0.6445 (pmm) cc_final: 0.6134 (pmm) REVERT: K 85 ASP cc_start: 0.6502 (p0) cc_final: 0.5892 (p0) REVERT: M 79 GLN cc_start: 0.7366 (tm-30) cc_final: 0.6262 (tm-30) REVERT: m 62 PHE cc_start: 0.6449 (m-80) cc_final: 0.5956 (m-80) outliers start: 2 outliers final: 1 residues processed: 458 average time/residue: 0.3452 time to fit residues: 257.1830 Evaluate side-chains 378 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 296 optimal weight: 9.9990 chunk 245 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 652 GLN H 39 GLN l 50 ASN l 51 ASN h 97 HIS A 67 ASN A 103 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN C 656 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN ** J 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26700 Z= 0.225 Angle : 0.699 13.633 36282 Z= 0.335 Chirality : 0.050 0.588 4353 Planarity : 0.004 0.057 4482 Dihedral : 13.225 109.446 5823 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.22 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.15), residues: 3090 helix: 0.79 (0.30), residues: 324 sheet: -0.80 (0.16), residues: 909 loop : -1.86 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 35 HIS 0.006 0.001 HIS G 374 PHE 0.013 0.002 PHE G 159 TYR 0.012 0.001 TYR h 59 ARG 0.007 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.8253 (tpt) cc_final: 0.7948 (tpt) REVERT: G 201 ILE cc_start: 0.8542 (tp) cc_final: 0.8158 (pt) REVERT: G 369 LEU cc_start: 0.8945 (tp) cc_final: 0.8668 (tt) REVERT: B 626 MET cc_start: 0.7084 (pmm) cc_final: 0.6843 (pmm) REVERT: H 85 ASP cc_start: 0.6548 (p0) cc_final: 0.6243 (p0) REVERT: h 53 LYS cc_start: 0.8099 (mmmm) cc_final: 0.7583 (mtpt) REVERT: h 70 SER cc_start: 0.6725 (t) cc_final: 0.6315 (m) REVERT: A 40 TYR cc_start: 0.7878 (t80) cc_final: 0.7447 (t80) REVERT: A 119 CYS cc_start: 0.6264 (m) cc_final: 0.6004 (m) REVERT: C 626 MET cc_start: 0.6739 (pmm) cc_final: 0.6471 (pmm) REVERT: D 31 ASP cc_start: 0.6601 (p0) cc_final: 0.6112 (p0) REVERT: D 85 ASP cc_start: 0.6938 (p0) cc_final: 0.6642 (p0) REVERT: e 61 ARG cc_start: 0.7338 (mtm180) cc_final: 0.6934 (mtm-85) REVERT: d 2 MET cc_start: 0.6317 (pmm) cc_final: 0.6038 (pmm) REVERT: J 622 ILE cc_start: 0.8065 (tp) cc_final: 0.7565 (tp) REVERT: J 626 MET cc_start: 0.6500 (pmm) cc_final: 0.6239 (pmm) REVERT: K 85 ASP cc_start: 0.6564 (p0) cc_final: 0.5912 (p0) REVERT: m 62 PHE cc_start: 0.6402 (m-80) cc_final: 0.6012 (m-80) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.3383 time to fit residues: 254.0105 Evaluate side-chains 379 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 249 optimal weight: 0.0040 chunk 165 optimal weight: 0.7980 chunk 294 optimal weight: 30.0000 chunk 184 optimal weight: 7.9990 chunk 179 optimal weight: 0.0010 chunk 136 optimal weight: 0.6980 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 GLN L 77 ASN h 97 HIS A 130 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 103 GLN ** J 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26700 Z= 0.175 Angle : 0.665 15.570 36282 Z= 0.316 Chirality : 0.048 0.390 4353 Planarity : 0.004 0.054 4482 Dihedral : 12.545 107.448 5823 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.35 % Favored : 92.49 % Rotamer: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3090 helix: 0.78 (0.30), residues: 324 sheet: -0.60 (0.17), residues: 873 loop : -1.80 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP l 35 HIS 0.004 0.001 HIS I 374 PHE 0.020 0.001 PHE I 53 TYR 0.012 0.001 TYR h 59 ARG 0.006 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 468 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8402 (tp) cc_final: 0.8029 (pt) REVERT: G 369 LEU cc_start: 0.8888 (tp) cc_final: 0.8537 (tt) REVERT: B 626 MET cc_start: 0.7202 (pmm) cc_final: 0.6963 (pmm) REVERT: H 37 VAL cc_start: 0.9112 (p) cc_final: 0.8880 (m) REVERT: H 38 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7646 (ttp-110) REVERT: H 85 ASP cc_start: 0.6185 (p0) cc_final: 0.5850 (p0) REVERT: L 87 ILE cc_start: 0.7211 (mt) cc_final: 0.6970 (mt) REVERT: h 53 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7745 (mtpp) REVERT: A 117 LYS cc_start: 0.8381 (mmtm) cc_final: 0.7881 (mmtp) REVERT: C 626 MET cc_start: 0.6532 (pmm) cc_final: 0.6247 (mtm) REVERT: D 31 ASP cc_start: 0.6740 (p0) cc_final: 0.6330 (p0) REVERT: D 85 ASP cc_start: 0.6695 (p0) cc_final: 0.6406 (p0) REVERT: e 61 ARG cc_start: 0.7296 (mtm180) cc_final: 0.6739 (mtm-85) REVERT: I 178 ARG cc_start: 0.7790 (tpt90) cc_final: 0.7481 (tpt90) REVERT: I 217 TYR cc_start: 0.8219 (m-80) cc_final: 0.7540 (m-80) REVERT: J 622 ILE cc_start: 0.8092 (tp) cc_final: 0.7611 (tp) REVERT: K 85 ASP cc_start: 0.6127 (p0) cc_final: 0.5493 (p0) REVERT: m 62 PHE cc_start: 0.6428 (m-80) cc_final: 0.5825 (m-80) outliers start: 2 outliers final: 1 residues processed: 469 average time/residue: 0.3442 time to fit residues: 260.7426 Evaluate side-chains 378 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 176 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 478 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN C 652 GLN C 656 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** J 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 26700 Z= 0.267 Angle : 0.716 14.755 36282 Z= 0.344 Chirality : 0.051 0.748 4353 Planarity : 0.004 0.056 4482 Dihedral : 12.365 107.019 5823 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.61 % Favored : 91.20 % Rotamer: Outliers : 0.04 % Allowed : 1.77 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3090 helix: 0.78 (0.30), residues: 324 sheet: -0.71 (0.16), residues: 894 loop : -1.84 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP m 35 HIS 0.006 0.001 HIS G 374 PHE 0.019 0.002 PHE G 159 TYR 0.019 0.001 TYR C 586 ARG 0.005 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 448 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.8242 (tpt) cc_final: 0.7755 (tpt) REVERT: G 201 ILE cc_start: 0.8371 (tp) cc_final: 0.7990 (pt) REVERT: G 369 LEU cc_start: 0.8927 (tp) cc_final: 0.8460 (tt) REVERT: B 626 MET cc_start: 0.7256 (pmm) cc_final: 0.7038 (pmm) REVERT: H 85 ASP cc_start: 0.6305 (p0) cc_final: 0.5927 (p0) REVERT: L 87 ILE cc_start: 0.7143 (mt) cc_final: 0.6902 (mt) REVERT: h 53 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7547 (mtpt) REVERT: A 117 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7820 (mmtp) REVERT: A 119 CYS cc_start: 0.6051 (m) cc_final: 0.5752 (m) REVERT: C 626 MET cc_start: 0.6538 (pmm) cc_final: 0.6088 (mtm) REVERT: C 630 GLN cc_start: 0.7688 (mt0) cc_final: 0.7123 (tt0) REVERT: D 31 ASP cc_start: 0.6884 (p0) cc_final: 0.6479 (p0) REVERT: D 85 ASP cc_start: 0.6956 (p0) cc_final: 0.6652 (p0) REVERT: e 61 ARG cc_start: 0.7304 (mtm180) cc_final: 0.6807 (mtm-85) REVERT: J 622 ILE cc_start: 0.8198 (tp) cc_final: 0.7711 (tp) REVERT: J 626 MET cc_start: 0.6481 (pmm) cc_final: 0.6063 (pmm) REVERT: J 638 TYR cc_start: 0.6658 (m-80) cc_final: 0.6390 (m-80) REVERT: K 85 ASP cc_start: 0.6404 (p0) cc_final: 0.5817 (p0) REVERT: m 62 PHE cc_start: 0.6417 (m-80) cc_final: 0.5866 (m-80) outliers start: 1 outliers final: 1 residues processed: 449 average time/residue: 0.3337 time to fit residues: 244.2939 Evaluate side-chains 374 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 259 optimal weight: 0.1980 chunk 273 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 GLN ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN h 97 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN I 195 ASN I 425 ASN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26700 Z= 0.218 Angle : 0.694 14.924 36282 Z= 0.331 Chirality : 0.049 0.571 4353 Planarity : 0.004 0.057 4482 Dihedral : 12.083 106.929 5823 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.86 % Favored : 91.94 % Rotamer: Outliers : 0.04 % Allowed : 0.85 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 3090 helix: 0.96 (0.30), residues: 312 sheet: -0.58 (0.17), residues: 849 loop : -1.74 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP m 35 HIS 0.004 0.001 HIS h 97 PHE 0.017 0.002 PHE G 53 TYR 0.015 0.001 TYR C 586 ARG 0.006 0.000 ARG l 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.8194 (tpt) cc_final: 0.7746 (tpt) REVERT: G 201 ILE cc_start: 0.8374 (tp) cc_final: 0.7987 (pt) REVERT: G 369 LEU cc_start: 0.8945 (tp) cc_final: 0.8490 (tt) REVERT: H 85 ASP cc_start: 0.6108 (p0) cc_final: 0.5768 (p0) REVERT: L 87 ILE cc_start: 0.7186 (mt) cc_final: 0.6859 (mt) REVERT: h 53 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7660 (mtpp) REVERT: A 117 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7890 (mmtp) REVERT: A 119 CYS cc_start: 0.6060 (m) cc_final: 0.5656 (m) REVERT: C 626 MET cc_start: 0.6446 (pmm) cc_final: 0.6230 (mtm) REVERT: D 31 ASP cc_start: 0.6825 (p0) cc_final: 0.6409 (p0) REVERT: D 85 ASP cc_start: 0.6575 (p0) cc_final: 0.6329 (p0) REVERT: e 37 GLN cc_start: 0.7583 (tm130) cc_final: 0.7323 (tm-30) REVERT: e 39 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7900 (mtp-110) REVERT: e 61 ARG cc_start: 0.7240 (mtm180) cc_final: 0.6853 (mtm-85) REVERT: d 2 MET cc_start: 0.5976 (pmm) cc_final: 0.5514 (pmm) REVERT: I 434 MET cc_start: 0.8240 (ptp) cc_final: 0.7985 (ptm) REVERT: J 622 ILE cc_start: 0.8157 (tp) cc_final: 0.7668 (tp) REVERT: J 626 MET cc_start: 0.6415 (pmm) cc_final: 0.6013 (pmm) REVERT: J 638 TYR cc_start: 0.6636 (m-80) cc_final: 0.6375 (m-80) REVERT: K 85 ASP cc_start: 0.6367 (p0) cc_final: 0.5746 (p0) REVERT: m 62 PHE cc_start: 0.6381 (m-80) cc_final: 0.5864 (m-80) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.3483 time to fit residues: 255.1899 Evaluate side-chains 366 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 6.9990 chunk 177 optimal weight: 0.0470 chunk 137 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 242 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN h 97 HIS A 374 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN C 656 ASN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN J 650 GLN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26700 Z= 0.178 Angle : 0.672 14.953 36282 Z= 0.319 Chirality : 0.048 0.494 4353 Planarity : 0.004 0.054 4482 Dihedral : 11.555 105.749 5823 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.35 % Favored : 92.49 % Rotamer: Outliers : 0.07 % Allowed : 0.37 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3090 helix: 0.92 (0.30), residues: 312 sheet: -0.58 (0.17), residues: 882 loop : -1.65 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 36 HIS 0.005 0.001 HIS h 97 PHE 0.014 0.001 PHE I 288 TYR 0.015 0.001 TYR C 586 ARG 0.006 0.000 ARG l 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 454 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.7996 (tpt) cc_final: 0.7542 (tpt) REVERT: G 201 ILE cc_start: 0.8525 (tp) cc_final: 0.7993 (pt) REVERT: G 369 LEU cc_start: 0.8927 (tp) cc_final: 0.8484 (tt) REVERT: B 626 MET cc_start: 0.6991 (pmm) cc_final: 0.6759 (pmm) REVERT: H 31 ASP cc_start: 0.7015 (p0) cc_final: 0.6773 (p0) REVERT: H 37 VAL cc_start: 0.9003 (p) cc_final: 0.8784 (m) REVERT: H 85 ASP cc_start: 0.6045 (p0) cc_final: 0.5626 (p0) REVERT: L 87 ILE cc_start: 0.7167 (mt) cc_final: 0.6956 (mt) REVERT: h 53 LYS cc_start: 0.7761 (mmmm) cc_final: 0.7441 (mtpt) REVERT: A 117 LYS cc_start: 0.8398 (mmtm) cc_final: 0.7842 (mmtp) REVERT: A 119 CYS cc_start: 0.5857 (m) cc_final: 0.5560 (m) REVERT: D 31 ASP cc_start: 0.6725 (p0) cc_final: 0.6246 (p0) REVERT: D 85 ASP cc_start: 0.6483 (p0) cc_final: 0.6251 (p0) REVERT: d 2 MET cc_start: 0.5918 (pmm) cc_final: 0.5426 (pmm) REVERT: I 119 CYS cc_start: 0.5896 (m) cc_final: 0.5687 (m) REVERT: I 178 ARG cc_start: 0.7825 (tpt90) cc_final: 0.7540 (tpt90) REVERT: I 217 TYR cc_start: 0.8029 (m-80) cc_final: 0.7335 (m-80) REVERT: I 434 MET cc_start: 0.8188 (ptp) cc_final: 0.7850 (ptm) REVERT: J 622 ILE cc_start: 0.8134 (tp) cc_final: 0.7650 (tp) REVERT: J 626 MET cc_start: 0.6484 (pmm) cc_final: 0.6052 (pmm) REVERT: K 31 ASP cc_start: 0.7123 (p0) cc_final: 0.6870 (p0) REVERT: K 85 ASP cc_start: 0.6360 (p0) cc_final: 0.5809 (p0) outliers start: 2 outliers final: 1 residues processed: 455 average time/residue: 0.3708 time to fit residues: 281.1744 Evaluate side-chains 376 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 375 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.246712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.241904 restraints weight = 34656.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.241336 restraints weight = 58680.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.240808 restraints weight = 61641.255| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26700 Z= 0.230 Angle : 0.693 14.674 36282 Z= 0.330 Chirality : 0.048 0.463 4353 Planarity : 0.004 0.053 4482 Dihedral : 11.417 105.459 5823 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.06 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3090 helix: 0.95 (0.31), residues: 312 sheet: -0.49 (0.17), residues: 852 loop : -1.70 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP l 35 HIS 0.005 0.001 HIS I 374 PHE 0.019 0.002 PHE I 468 TYR 0.014 0.001 TYR C 586 ARG 0.016 0.000 ARG l 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5097.83 seconds wall clock time: 98 minutes 59.92 seconds (5939.92 seconds total)