Starting phenix.real_space_refine on Sat Mar 23 02:55:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw6_24064/03_2024/7mw6_24064.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw6_24064/03_2024/7mw6_24064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw6_24064/03_2024/7mw6_24064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw6_24064/03_2024/7mw6_24064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw6_24064/03_2024/7mw6_24064.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw6_24064/03_2024/7mw6_24064.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 22362 2.51 5 N 5778 2.21 5 O 6954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35247 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 8166 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8157 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8157 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8338 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8153 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8153 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8334 Chain: "B" Number of atoms: 8170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8161 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8161 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8342 Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 residue: pdb=" N AGLN C1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 Time building chain proxies: 27.47, per 1000 atoms: 0.78 Number of scatterers: 35247 At special positions: 0 Unit cell: (168.744, 156.996, 247.776, 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 153 16.00 O 6954 8.00 N 5778 7.00 C 22362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.04 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 190 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.04 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 245 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG j 1 " - " NAG j 2 " " NAG p 1 " - " NAG p 2 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A1074 " " NAG A1307 " - " ASN A 234 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 234 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C1074 " " NAG C1307 " - " ASN C 234 " " NAG I 1 " - " ASN A 61 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 122 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 709 " " NAG S 1 " - " ASN A 343 " " NAG T 1 " - " ASN A 17 " " NAG U 1 " - " ASN C 61 " " NAG V 1 " - " ASN C 282 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 709 " " NAG d 1 " - " ASN C 343 " " NAG e 1 " - " ASN C 17 " " NAG f 1 " - " ASN B 61 " " NAG g 1 " - " ASN B 282 " " NAG h 1 " - " ASN B 122 " " NAG i 1 " - " ASN B 331 " " NAG j 1 " - " ASN B1134 " " NAG k 1 " - " ASN B1098 " " NAG l 1 " - " ASN B 801 " " NAG m 1 " - " ASN B 717 " " NAG n 1 " - " ASN B 709 " " NAG o 1 " - " ASN B 343 " " NAG p 1 " - " ASN B 17 " Time building additional restraints: 12.80 Conformation dependent library (CDL) restraints added in 10.1 seconds 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8298 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 80 sheets defined 19.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.967A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.707A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.503A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.622A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.375A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.654A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.599A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.502A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 920 removed outlier: 3.670A pdb=" N GLN A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 941 removed outlier: 5.883A pdb=" N PHE A 927 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.528A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.565A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.526A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.411A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 236 through 240 removed outlier: 4.240A pdb=" N GLY D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 236 through 240' Processing helix chain 'L' and resid 172 through 179 removed outlier: 3.669A pdb=" N GLY L 179 " --> pdb=" O GLN L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 239 Processing helix chain 'H' and resid 236 through 242 removed outlier: 4.031A pdb=" N GLY H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.329A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.751A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.017A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.631A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.852A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.618A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.571A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.577A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.701A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 916 through 920 removed outlier: 3.572A pdb=" N GLN C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 941 removed outlier: 6.340A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.758A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.107A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.559A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.513A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.543A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.847A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.581A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.611A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.726A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 909 removed outlier: 3.585A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 920 removed outlier: 3.506A pdb=" N GLN B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 941 removed outlier: 5.910A pdb=" N PHE B 927 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.571A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.555A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.741A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.458A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'F' and resid 236 through 242 removed outlier: 4.106A pdb=" N GLY F 240 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.972A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.789A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.383A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.311A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.556A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 328 removed outlier: 4.823A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.654A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 714 Processing sheet with id=AB5, first strand: chain 'A' and resid 721 through 728 removed outlier: 7.126A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.880A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1080 through 1082 Processing sheet with id=AB9, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC1, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC2, first strand: chain 'E' and resid 30 through 33 Processing sheet with id=AC3, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AC4, first strand: chain 'E' and resid 165 through 169 removed outlier: 3.819A pdb=" N SER E 165 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 226 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN E 189 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR E 224 " --> pdb=" O ASN E 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 195 through 201 Processing sheet with id=AC6, first strand: chain 'D' and resid 24 through 26 removed outlier: 4.006A pdb=" N SER D 40 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.617A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET D 53 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.085A pdb=" N TYR D 226 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.085A pdb=" N TYR D 226 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 201 through 204 removed outlier: 4.727A pdb=" N TYR D 244 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 25 through 27 Processing sheet with id=AD3, first strand: chain 'L' and resid 30 through 33 removed outlier: 3.667A pdb=" N THR L 126 " --> pdb=" O TYR L 110 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR L 110 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN L 61 " --> pdb=" O LYS L 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AD5, first strand: chain 'L' and resid 165 through 169 removed outlier: 3.988A pdb=" N SER L 165 " --> pdb=" O ASN L 188 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER L 182 " --> pdb=" O LEU L 232 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU L 232 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL L 184 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU L 230 " --> pdb=" O VAL L 184 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 186 " --> pdb=" O SER L 228 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER L 228 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN L 188 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU L 226 " --> pdb=" O ASN L 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 195 through 201 Processing sheet with id=AD7, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.883A pdb=" N SER H 40 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.891A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET H 53 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.991A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.991A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 201 through 204 removed outlier: 4.603A pdb=" N TYR H 244 " --> pdb=" O VAL H 261 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.024A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.045A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.914A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.862A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.042A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.004A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.212A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.091A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF6, first strand: chain 'C' and resid 721 through 728 removed outlier: 6.819A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.960A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG1, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AG2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.873A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.773A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AG6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AG7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.454A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.766A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.335A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.575A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.042A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.338A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AH7, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AH8, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AH9, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.873A pdb=" N GLN G 58 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AI2, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.201A pdb=" N SER G 182 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU G 232 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL G 184 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU G 230 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU G 186 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER G 228 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASN G 188 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU G 226 " --> pdb=" O ASN G 188 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 195 through 201 Processing sheet with id=AI4, first strand: chain 'F' and resid 24 through 26 removed outlier: 4.090A pdb=" N SER F 40 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 77 through 79 removed outlier: 5.727A pdb=" N TRP F 66 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS F 57 " --> pdb=" O TRP F 66 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.134A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.134A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 201 through 204 removed outlier: 4.556A pdb=" N TYR F 244 " --> pdb=" O VAL F 261 " (cutoff:3.500A) 1342 hydrogen bonds defined for protein. 3612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.82 Time building geometry restraints manager: 14.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5970 1.32 - 1.45: 9923 1.45 - 1.57: 19944 1.57 - 1.70: 1 1.70 - 1.82: 198 Bond restraints: 36036 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.512 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 36031 not shown) Histogram of bond angle deviations from ideal: 81.63 - 92.26: 1 92.26 - 102.89: 203 102.89 - 113.52: 21081 113.52 - 124.15: 27063 124.15 - 134.78: 729 Bond angle restraints: 49077 Sorted by residual: angle pdb=" C LEU B 24 " pdb=" N PRO B 25 " pdb=" CD PRO B 25 " ideal model delta sigma weight residual 125.00 81.63 43.37 4.10e+00 5.95e-02 1.12e+02 angle pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 111.33 121.92 -10.59 1.43e+00 4.89e-01 5.49e+01 angle pdb=" C GLY C 252 " pdb=" N ASP C 253 " pdb=" CA ASP C 253 " ideal model delta sigma weight residual 121.54 134.78 -13.24 1.91e+00 2.74e-01 4.81e+01 angle pdb=" N GLU B1072 " pdb=" CA GLU B1072 " pdb=" C GLU B1072 " ideal model delta sigma weight residual 110.80 125.51 -14.71 2.13e+00 2.20e-01 4.77e+01 angle pdb=" C SER H 118 " pdb=" CA SER H 118 " pdb=" CB SER H 118 " ideal model delta sigma weight residual 116.54 109.49 7.05 1.15e+00 7.56e-01 3.76e+01 ... (remaining 49072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 21486 27.09 - 54.18: 866 54.18 - 81.27: 134 81.27 - 108.37: 86 108.37 - 135.46: 24 Dihedral angle restraints: 22596 sinusoidal: 9687 harmonic: 12909 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 -178.60 -88.40 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CA LYS C 811 " pdb=" C LYS C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta harmonic sigma weight residual 180.00 135.55 44.45 0 5.00e+00 4.00e-02 7.90e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -164.97 78.97 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 22593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.527: 5832 0.527 - 1.055: 6 1.055 - 1.582: 2 1.582 - 2.110: 0 2.110 - 2.637: 4 Chirality restraints: 5844 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 0.24 -2.64 2.00e-01 2.50e+01 1.74e+02 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 0.12 -2.52 2.00e-01 2.50e+01 1.59e+02 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 0.09 -2.49 2.00e-01 2.50e+01 1.56e+02 ... (remaining 5841 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.301 2.00e-02 2.50e+03 2.58e-01 8.33e+02 pdb=" C7 NAG B1305 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.261 2.00e-02 2.50e+03 2.18e-01 5.91e+02 pdb=" C7 NAG B1302 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.363 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " 0.256 2.00e-02 2.50e+03 2.13e-01 5.67e+02 pdb=" C7 NAG C1302 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.008 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.22: 12 2.22 - 2.89: 14085 2.89 - 3.56: 48445 3.56 - 4.23: 84213 4.23 - 4.90: 140536 Nonbonded interactions: 287291 Sorted by model distance: nonbonded pdb=" ND2 ASN B1074 " pdb=" C1 NAG B1305 " model vdw 1.556 3.550 nonbonded pdb=" ND2 ASN A1074 " pdb=" C1 NAG A1306 " model vdw 1.561 3.550 nonbonded pdb=" ND2 ASN C1074 " pdb=" C1 NAG C1306 " model vdw 1.562 3.550 nonbonded pdb=" O GLY F 27 " pdb=" OG1 THR F 127 " model vdw 2.093 2.440 nonbonded pdb=" OD1 ASN C 125 " pdb=" O3 NAG W 1 " model vdw 2.104 2.440 ... (remaining 287286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 181 or (resid 182 through 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 416 or (resid 417 a \ nd (name N or name CA or name C or name O or name CB )) or resid 418 through 100 \ 9 or resid 1011 through 1145 or resid 1301 through 1307)) selection = (chain 'B' and (resid 15 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 181 or (resid 182 through 183 a \ nd (name N or name CA or name C or name O or name CB )) or resid 184 through 416 \ or (resid 417 and (name N or name CA or name C or name O or name CB )) or resid \ 418 through 1009 or resid 1011 through 1145 or resid 1301 through 1307)) selection = (chain 'C' and (resid 15 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 1009 or resid 1011 through 1145 \ or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.200 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 104.530 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.005 0.106 36036 Z= 0.305 Angle : 0.837 43.373 49077 Z= 0.449 Chirality : 0.092 2.637 5844 Planarity : 0.010 0.258 6213 Dihedral : 16.604 135.458 14145 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.08 % Favored : 94.23 % Rotamer: Outliers : 0.13 % Allowed : 0.35 % Favored : 99.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.07 % 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: -1.15 (0.12), residues: 4395 helix: -0.07 (0.19), residues: 725 sheet: -0.07 (0.14), residues: 1321 loop : -1.41 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 152 HIS 0.011 0.001 HIS B 69 PHE 0.039 0.002 PHE B 135 TYR 0.023 0.002 TYR L 73 ARG 0.008 0.001 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 420 time to evaluate : 4.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8302 (mp) cc_final: 0.7752 (mp) REVERT: E 22 ILE cc_start: 0.6684 (mp) cc_final: 0.6402 (mp) REVERT: D 125 GLN cc_start: 0.6810 (pm20) cc_final: 0.6602 (pm20) REVERT: L 59 TRP cc_start: 0.6417 (m-10) cc_final: 0.5847 (m-10) REVERT: B 490 PHE cc_start: 0.7173 (t80) cc_final: 0.6938 (t80) REVERT: F 250 HIS cc_start: -0.0180 (t-170) cc_final: -0.0856 (t-90) outliers start: 2 outliers final: 1 residues processed: 421 average time/residue: 0.4579 time to fit residues: 322.5236 Evaluate side-chains 331 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 113 optimal weight: 0.0040 chunk 223 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 343 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 chunk 397 optimal weight: 20.0000 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 ASN L 217 GLN H 54 ASN H 71 ASN C 66 HIS C 394 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1010 GLN B B 394 ASN B 901 GLN B1010 GLN B G 175 GLN ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 36036 Z= 0.378 Angle : 0.805 25.411 49077 Z= 0.395 Chirality : 0.057 0.721 5844 Planarity : 0.007 0.182 6213 Dihedral : 14.267 115.567 6566 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.00 % Favored : 93.30 % Rotamer: Outliers : 0.72 % Allowed : 7.05 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4395 helix: 0.64 (0.19), residues: 705 sheet: -0.13 (0.14), residues: 1333 loop : -1.34 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 258 HIS 0.014 0.002 HIS B 69 PHE 0.044 0.003 PHE A 906 TYR 0.031 0.002 TYR E 73 ARG 0.010 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 367 time to evaluate : 3.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 ARG cc_start: 0.6196 (ttt90) cc_final: 0.5703 (ttt90) REVERT: G 126 THR cc_start: 0.5880 (OUTLIER) cc_final: 0.5472 (p) REVERT: F 117 ARG cc_start: 0.6755 (tmm-80) cc_final: 0.6555 (ttm-80) REVERT: F 250 HIS cc_start: -0.0210 (t-170) cc_final: -0.0787 (t-90) outliers start: 24 outliers final: 16 residues processed: 378 average time/residue: 0.4152 time to fit residues: 262.2802 Evaluate side-chains 356 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 339 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 189 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain G residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 331 optimal weight: 0.0970 chunk 270 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 398 optimal weight: 20.0000 chunk 430 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 395 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 134 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 24 GLN D 81 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 ASN ** L 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 394 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 36036 Z= 0.339 Angle : 0.762 16.591 49077 Z= 0.375 Chirality : 0.055 0.689 5844 Planarity : 0.006 0.155 6213 Dihedral : 13.062 114.092 6564 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.86 % Favored : 93.50 % Rotamer: Outliers : 1.07 % Allowed : 9.13 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 4395 helix: 0.89 (0.20), residues: 699 sheet: -0.16 (0.14), residues: 1341 loop : -1.30 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 258 HIS 0.009 0.001 HIS C1064 PHE 0.031 0.002 PHE F 48 TYR 0.022 0.002 TYR C1067 ARG 0.009 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 363 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 TRP cc_start: 0.5270 (m-10) cc_final: 0.4876 (m-10) REVERT: D 117 ARG cc_start: 0.6159 (ttt90) cc_final: 0.5397 (ttt90) REVERT: B 581 THR cc_start: 0.6951 (p) cc_final: 0.6706 (p) REVERT: F 250 HIS cc_start: -0.0227 (t-170) cc_final: -0.0751 (t-90) outliers start: 37 outliers final: 29 residues processed: 384 average time/residue: 0.4391 time to fit residues: 281.9331 Evaluate side-chains 369 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 340 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 189 ASN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 206 optimal weight: 0.2980 chunk 44 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 267 optimal weight: 0.6980 chunk 399 optimal weight: 8.9990 chunk 423 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 379 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 ASN L 250 GLN C 66 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 388 ASN B 394 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 36036 Z= 0.275 Angle : 0.727 14.162 49077 Z= 0.357 Chirality : 0.053 0.668 5844 Planarity : 0.006 0.148 6213 Dihedral : 11.741 112.545 6564 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.72 % Favored : 93.64 % Rotamer: Outliers : 1.28 % Allowed : 10.57 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 4395 helix: 1.01 (0.20), residues: 704 sheet: -0.21 (0.14), residues: 1360 loop : -1.24 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 123 HIS 0.015 0.001 HIS E 100 PHE 0.030 0.002 PHE F 48 TYR 0.021 0.002 TYR C1067 ARG 0.006 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 362 time to evaluate : 3.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 396 TYR cc_start: 0.7224 (m-80) cc_final: 0.6975 (m-80) REVERT: B 581 THR cc_start: 0.6968 (p) cc_final: 0.6716 (p) REVERT: F 46 TYR cc_start: 0.4344 (m-80) cc_final: 0.3562 (m-80) outliers start: 45 outliers final: 34 residues processed: 389 average time/residue: 0.4596 time to fit residues: 299.8136 Evaluate side-chains 374 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 340 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 189 ASN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 315 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 292 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 ASN C 66 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS B 394 ASN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 36036 Z= 0.366 Angle : 0.757 24.393 49077 Z= 0.372 Chirality : 0.054 0.633 5844 Planarity : 0.006 0.179 6213 Dihedral : 11.021 111.234 6564 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.13 % Favored : 93.30 % Rotamer: Outliers : 1.76 % Allowed : 11.24 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 4395 helix: 0.82 (0.19), residues: 723 sheet: -0.17 (0.13), residues: 1377 loop : -1.29 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 258 HIS 0.009 0.001 HIS C1064 PHE 0.043 0.002 PHE F 48 TYR 0.023 0.002 TYR C1067 ARG 0.009 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 374 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 ASP cc_start: 0.6630 (t0) cc_final: 0.6425 (t70) REVERT: H 100 MET cc_start: 0.5719 (tmm) cc_final: 0.5310 (tmm) REVERT: B 581 THR cc_start: 0.6971 (p) cc_final: 0.6724 (p) REVERT: G 98 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.6921 (p0) REVERT: F 174 LEU cc_start: 0.4016 (OUTLIER) cc_final: 0.3776 (mt) outliers start: 63 outliers final: 44 residues processed: 411 average time/residue: 0.4303 time to fit residues: 298.0712 Evaluate side-chains 392 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 346 time to evaluate : 3.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 174 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 10.0000 chunk 381 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 248 optimal weight: 0.0470 chunk 104 optimal weight: 1.9990 chunk 423 optimal weight: 0.9980 chunk 351 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 35 optimal weight: 0.0070 chunk 140 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS B 394 ASN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36036 Z= 0.195 Angle : 0.698 18.612 49077 Z= 0.339 Chirality : 0.050 0.605 5844 Planarity : 0.006 0.159 6213 Dihedral : 10.097 109.345 6564 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.34 % Favored : 94.07 % Rotamer: Outliers : 1.44 % Allowed : 11.77 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4395 helix: 1.36 (0.20), residues: 698 sheet: -0.09 (0.14), residues: 1332 loop : -1.19 (0.13), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP H 123 HIS 0.034 0.001 HIS C1058 PHE 0.045 0.001 PHE F 48 TYR 0.020 0.001 TYR D 114 ARG 0.009 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 363 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 MET cc_start: 0.5475 (tmm) cc_final: 0.5148 (tmm) REVERT: C 455 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7703 (mt) REVERT: B 581 THR cc_start: 0.6923 (p) cc_final: 0.6668 (p) REVERT: G 190 PHE cc_start: 0.3484 (p90) cc_final: 0.2799 (p90) outliers start: 51 outliers final: 39 residues processed: 392 average time/residue: 0.4428 time to fit residues: 292.7893 Evaluate side-chains 383 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 343 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 125 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 239 optimal weight: 0.0060 chunk 356 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 422 optimal weight: 0.8980 chunk 264 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 36036 Z= 0.328 Angle : 0.739 16.319 49077 Z= 0.363 Chirality : 0.052 0.594 5844 Planarity : 0.006 0.150 6213 Dihedral : 9.801 108.591 6564 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.97 % Favored : 93.46 % Rotamer: Outliers : 1.65 % Allowed : 12.25 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4395 helix: 1.20 (0.20), residues: 705 sheet: -0.12 (0.14), residues: 1386 loop : -1.19 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP H 123 HIS 0.007 0.001 HIS C1064 PHE 0.028 0.002 PHE F 48 TYR 0.033 0.002 TYR E 191 ARG 0.007 0.001 ARG G 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 350 time to evaluate : 3.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 228 LEU cc_start: 0.1696 (OUTLIER) cc_final: 0.1441 (pp) REVERT: H 100 MET cc_start: 0.5418 (tmm) cc_final: 0.5164 (tmm) REVERT: B 581 THR cc_start: 0.6944 (p) cc_final: 0.6693 (p) REVERT: G 98 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.6949 (p0) REVERT: G 190 PHE cc_start: 0.3391 (p90) cc_final: 0.2753 (p90) outliers start: 59 outliers final: 48 residues processed: 385 average time/residue: 0.4341 time to fit residues: 283.1901 Evaluate side-chains 388 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 338 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 119 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 287 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 331 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36036 Z= 0.214 Angle : 0.695 15.147 49077 Z= 0.340 Chirality : 0.050 0.577 5844 Planarity : 0.006 0.146 6213 Dihedral : 9.229 106.648 6564 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.56 % Favored : 93.87 % Rotamer: Outliers : 1.33 % Allowed : 12.92 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4395 helix: 1.40 (0.20), residues: 704 sheet: -0.05 (0.14), residues: 1371 loop : -1.18 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP H 123 HIS 0.004 0.001 HIS C1064 PHE 0.023 0.001 PHE F 172 TYR 0.021 0.001 TYR L 73 ARG 0.009 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 355 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 MET cc_start: 0.5313 (tmm) cc_final: 0.5097 (tmm) REVERT: B 595 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8594 (t) REVERT: G 98 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.6943 (p0) REVERT: G 190 PHE cc_start: 0.3219 (p90) cc_final: 0.2676 (p90) outliers start: 47 outliers final: 39 residues processed: 382 average time/residue: 0.4269 time to fit residues: 276.3805 Evaluate side-chains 382 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 341 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 0.7980 chunk 404 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 393 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 308 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 355 optimal weight: 3.9990 chunk 372 optimal weight: 1.9990 chunk 392 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36036 Z= 0.205 Angle : 0.684 14.666 49077 Z= 0.337 Chirality : 0.050 0.575 5844 Planarity : 0.006 0.147 6213 Dihedral : 8.810 104.916 6564 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.61 % Favored : 93.78 % Rotamer: Outliers : 1.36 % Allowed : 12.84 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4395 helix: 1.54 (0.20), residues: 703 sheet: 0.01 (0.14), residues: 1358 loop : -1.17 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP H 123 HIS 0.008 0.001 HIS F 250 PHE 0.032 0.001 PHE F 172 TYR 0.032 0.001 TYR F 46 ARG 0.007 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 358 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 228 LEU cc_start: 0.1213 (OUTLIER) cc_final: 0.1011 (pp) REVERT: B 595 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8595 (t) REVERT: G 98 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.6879 (p0) REVERT: G 190 PHE cc_start: 0.3192 (p90) cc_final: 0.2815 (p90) outliers start: 48 outliers final: 42 residues processed: 388 average time/residue: 0.4195 time to fit residues: 274.4570 Evaluate side-chains 385 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 340 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain H residue 123 TRP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 2.9990 chunk 415 optimal weight: 8.9990 chunk 253 optimal weight: 0.0470 chunk 197 optimal weight: 6.9990 chunk 289 optimal weight: 0.6980 chunk 436 optimal weight: 20.0000 chunk 401 optimal weight: 0.3980 chunk 347 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 762 GLN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 36036 Z= 0.256 Angle : 0.706 14.750 49077 Z= 0.348 Chirality : 0.050 0.564 5844 Planarity : 0.006 0.148 6213 Dihedral : 8.747 103.846 6564 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.68 % Favored : 93.73 % Rotamer: Outliers : 1.41 % Allowed : 13.29 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 4395 helix: 1.32 (0.20), residues: 721 sheet: 0.01 (0.14), residues: 1359 loop : -1.19 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP H 123 HIS 0.006 0.001 HIS A 69 PHE 0.034 0.002 PHE G 111 TYR 0.022 0.002 TYR L 73 ARG 0.009 0.001 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 350 time to evaluate : 4.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 GLN cc_start: 0.6992 (pm20) cc_final: 0.6788 (pm20) REVERT: D 228 LEU cc_start: 0.1254 (OUTLIER) cc_final: 0.1051 (pp) REVERT: B 595 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8603 (t) REVERT: G 98 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.6890 (p0) REVERT: G 190 PHE cc_start: 0.3242 (p90) cc_final: 0.2724 (p90) outliers start: 50 outliers final: 42 residues processed: 380 average time/residue: 0.4297 time to fit residues: 277.1057 Evaluate side-chains 389 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 344 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain H residue 123 TRP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 0.9990 chunk 370 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 320 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 348 optimal weight: 0.5980 chunk 145 optimal weight: 10.0000 chunk 357 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.110944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085372 restraints weight = 198607.144| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 6.70 r_work: 0.2693 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 36036 Z= 0.221 Angle : 0.692 14.712 49077 Z= 0.341 Chirality : 0.050 0.568 5844 Planarity : 0.006 0.148 6213 Dihedral : 8.624 102.938 6564 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.61 % Favored : 93.80 % Rotamer: Outliers : 1.36 % Allowed : 13.34 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4395 helix: 1.48 (0.20), residues: 703 sheet: 0.03 (0.14), residues: 1360 loop : -1.17 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP H 123 HIS 0.006 0.001 HIS A 69 PHE 0.030 0.001 PHE E 122 TYR 0.027 0.001 TYR E 60 ARG 0.010 0.001 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7738.23 seconds wall clock time: 142 minutes 22.58 seconds (8542.58 seconds total)