Starting phenix.real_space_refine (version: dev) on Mon Feb 27 14:04:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws3_32742/02_2023/7ws3_32742.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws3_32742/02_2023/7ws3_32742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws3_32742/02_2023/7ws3_32742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws3_32742/02_2023/7ws3_32742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws3_32742/02_2023/7ws3_32742.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws3_32742/02_2023/7ws3_32742.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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 Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 99": "OD1" <-> "OD2" Residue "I GLU 103": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30215 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8063 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 8048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8048 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8053 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 52, 'TRANS': 986} Chain breaks: 7 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.70, per 1000 atoms: 0.55 Number of scatterers: 30215 At special positions: 0 Unit cell: (150.06, 136.12, 210.74, 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 138 16.00 O 5920 8.00 N 4966 7.00 C 19191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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 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=2.04 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 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=2.04 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=2.04 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=2.02 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 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 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 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-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN A 343 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 343 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 12.34 Conformation dependent library (CDL) restraints added in 4.6 seconds 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7106 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 73 sheets defined 21.6% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.517A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.190A 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 removed outlier: 3.593A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.702A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.855A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.524A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.562A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.976A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.542A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.158A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.847A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.124A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.268A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.953A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.707A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.046A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.707A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.728A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.955A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.668A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.973A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.416A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.666A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.310A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.847A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.735A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.754A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.725A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.902A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.965A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.833A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.310A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.772A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.019A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.986A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.818A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.988A pdb=" N ASP I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.363A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.218A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.218A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.509A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.529A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.602A pdb=" N ASP A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 156 " --> pdb=" O ASP A 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.055A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.853A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.703A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.694A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.512A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.571A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.433A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.522A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.574A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 132 through 142 removed outlier: 4.291A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP B 138 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLY B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.198A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.956A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.546A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.828A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.354A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.508A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.585A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.891A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.548A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.521A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.655A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.427A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 133 through 135 removed outlier: 4.248A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.333A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.238A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.266A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.554A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.553A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.553A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.664A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.710A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AG1, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.922A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.744A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.677A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR E 112 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.677A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR E 94 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.708A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AG8, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.923A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.744A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AH2, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR G 112 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR G 94 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.711A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AH6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.923A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR H 98 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.745A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR I 112 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR I 94 " --> pdb=" O THR I 117 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3138 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: 16.41 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8061 1.33 - 1.46: 8462 1.46 - 1.59: 14189 1.59 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 30889 Sorted by residual: bond pdb=" N THR E 106 " pdb=" CA THR E 106 " ideal model delta sigma weight residual 1.453 1.487 -0.033 9.20e-03 1.18e+04 1.32e+01 bond pdb=" C PRO B 986 " pdb=" O PRO B 986 " ideal model delta sigma weight residual 1.240 1.205 0.035 1.12e-02 7.97e+03 9.91e+00 bond pdb=" N GLU E 103 " pdb=" CA GLU E 103 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.44e+00 bond pdb=" C ASP B 985 " pdb=" N PRO B 986 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.32e+00 bond pdb=" N ARG H 18 " pdb=" CA ARG H 18 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.20e-02 6.94e+03 8.17e+00 ... (remaining 30884 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.30: 588 105.30 - 112.51: 15841 112.51 - 119.71: 9959 119.71 - 126.91: 15340 126.91 - 134.11: 312 Bond angle restraints: 42040 Sorted by residual: angle pdb=" CA PRO B 986 " pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 117.93 123.20 -5.27 1.20e+00 6.94e-01 1.93e+01 angle pdb=" CB ARG C 452 " pdb=" CG ARG C 452 " pdb=" CD ARG C 452 " ideal model delta sigma weight residual 111.30 119.62 -8.32 2.30e+00 1.89e-01 1.31e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.98 -4.28 1.22e+00 6.72e-01 1.23e+01 angle pdb=" CB LYS C 814 " pdb=" CG LYS C 814 " pdb=" CD LYS C 814 " ideal model delta sigma weight residual 111.30 119.06 -7.76 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA LEU B 461 " pdb=" CB LEU B 461 " pdb=" CG LEU B 461 " ideal model delta sigma weight residual 116.30 128.01 -11.71 3.50e+00 8.16e-02 1.12e+01 ... (remaining 42035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 16709 17.86 - 35.72: 1240 35.72 - 53.57: 219 53.57 - 71.43: 36 71.43 - 89.29: 27 Dihedral angle restraints: 18231 sinusoidal: 7174 harmonic: 11057 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.05 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.94 88.94 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -171.66 85.66 1 1.00e+01 1.00e-02 8.87e+01 ... (remaining 18228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4882 0.140 - 0.280: 20 0.280 - 0.419: 1 0.419 - 0.559: 2 0.559 - 0.699: 1 Chirality restraints: 4906 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 4903 not shown) Planarity restraints: 5416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 874 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C THR C 874 " 0.057 2.00e-02 2.50e+03 pdb=" O THR C 874 " -0.021 2.00e-02 2.50e+03 pdb=" N SER C 875 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.053 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO A 337 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.58e+00 pdb=" N PRO C 337 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.039 5.00e-02 4.00e+02 ... (remaining 5413 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2296 2.74 - 3.28: 28655 3.28 - 3.82: 46722 3.82 - 4.36: 54176 4.36 - 4.90: 97237 Nonbonded interactions: 229086 Sorted by model distance: nonbonded pdb=" NH2 ARG A 403 " pdb=" OD2 ASP A 405 " model vdw 2.202 2.520 nonbonded pdb=" ND2 ASN A 439 " pdb=" OH TYR D 32 " model vdw 2.207 2.520 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.233 2.520 nonbonded pdb=" NH1 ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 2.258 2.520 nonbonded pdb=" NH1 ARG H 61 " pdb=" OD2 ASP H 82 " model vdw 2.258 2.520 ... (remaining 229081 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 108 or (resid 109 through 110 and (name N or na \ me CA or name C or name O or name CB )) or resid 111 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 or (resid 5 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 557 through \ 827 or resid 854 through 984 or (resid 985 and (name N or name CA or name C or \ name O or name CB )) or resid 986 through 1044 or (resid 1045 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1046 through 1147 or resid 1301 \ through 1307)) selection = (chain 'B' and (resid 15 through 555 or (resid 556 and (name N or name CA or nam \ e C or name O or name CB )) or resid 557 or (resid 558 through 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 785 or (resid 7 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 787 through \ 827 or (resid 854 and (name N or name CA or name C or name O or name CB )) or r \ esid 855 through 903 or (resid 904 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ ) \ ) or resid 905 through 1044 or (resid 1045 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1046 through 1147 or resid 1301 through 1307)) selection = (chain 'C' and (resid 15 through 108 or (resid 109 through 110 and (name N or na \ me CA or name C or name O or name CB )) or resid 111 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 557 \ or (resid 558 through 559 and (name N or name CA or name C or name O or name CB \ )) or resid 560 through 827 or resid 854 through 903 or (resid 904 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 905 through 984 or (resid 985 and (n \ ame N or name CA or name C or name O or name CB )) or resid 986 through 1147 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 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 19191 2.51 5 N 4966 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 30.520 Check model and map are aligned: 0.540 Process input model: 82.160 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Set scattering table: 0.250 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 30889 Z= 0.195 Angle : 0.612 11.706 42040 Z= 0.330 Chirality : 0.046 0.699 4906 Planarity : 0.004 0.082 5377 Dihedral : 12.978 89.288 10996 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3751 helix: 0.98 (0.21), residues: 673 sheet: -0.34 (0.16), residues: 1049 loop : -1.32 (0.13), residues: 2029 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.4500 time to fit residues: 312.3715 Evaluate side-chains 249 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 3.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 341 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 762 GLN C 774 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 37 GLN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 30889 Z= 0.238 Angle : 0.592 9.413 42040 Z= 0.311 Chirality : 0.047 0.649 4906 Planarity : 0.004 0.051 5377 Dihedral : 4.508 26.334 4410 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3751 helix: 1.49 (0.21), residues: 667 sheet: -0.27 (0.16), residues: 1091 loop : -1.36 (0.13), residues: 1993 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 268 time to evaluate : 3.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 290 average time/residue: 0.4294 time to fit residues: 202.2677 Evaluate side-chains 251 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 3.533 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2748 time to fit residues: 16.0385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 284 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 342 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 339 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN H 27 GLN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.056 30889 Z= 0.536 Angle : 0.739 11.186 42040 Z= 0.390 Chirality : 0.051 0.664 4906 Planarity : 0.005 0.051 5377 Dihedral : 5.226 29.154 4410 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3751 helix: 1.22 (0.21), residues: 657 sheet: -0.70 (0.15), residues: 1133 loop : -1.64 (0.13), residues: 1961 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 241 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 272 average time/residue: 0.4145 time to fit residues: 186.8491 Evaluate side-chains 227 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 3.583 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2684 time to fit residues: 16.3397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 343 optimal weight: 40.0000 chunk 363 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 325 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 762 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30889 Z= 0.227 Angle : 0.572 9.471 42040 Z= 0.300 Chirality : 0.046 0.615 4906 Planarity : 0.004 0.048 5377 Dihedral : 4.818 28.887 4410 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 3751 helix: 1.53 (0.21), residues: 672 sheet: -0.45 (0.16), residues: 1050 loop : -1.50 (0.13), residues: 2029 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 265 average time/residue: 0.4122 time to fit residues: 183.6955 Evaluate side-chains 229 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 3.753 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3431 time to fit residues: 14.6718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 270 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 310 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 30889 Z= 0.313 Angle : 0.594 9.340 42040 Z= 0.311 Chirality : 0.046 0.613 4906 Planarity : 0.004 0.048 5377 Dihedral : 4.832 28.344 4410 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3751 helix: 1.61 (0.21), residues: 668 sheet: -0.46 (0.16), residues: 1047 loop : -1.50 (0.13), residues: 2036 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 225 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 23 residues processed: 266 average time/residue: 0.4174 time to fit residues: 186.3629 Evaluate side-chains 232 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 209 time to evaluate : 3.539 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2796 time to fit residues: 17.1092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 363 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 774 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 30889 Z= 0.177 Angle : 0.544 10.429 42040 Z= 0.281 Chirality : 0.045 0.684 4906 Planarity : 0.004 0.045 5377 Dihedral : 4.593 27.308 4410 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3751 helix: 1.82 (0.21), residues: 672 sheet: -0.30 (0.16), residues: 1033 loop : -1.40 (0.13), residues: 2046 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 248 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 274 average time/residue: 0.4238 time to fit residues: 196.5650 Evaluate side-chains 233 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 221 time to evaluate : 3.946 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.3049 time to fit residues: 11.7925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 207 optimal weight: 30.0000 chunk 265 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 chunk 226 optimal weight: 0.0870 chunk 220 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 30889 Z= 0.294 Angle : 0.591 10.964 42040 Z= 0.304 Chirality : 0.046 0.654 4906 Planarity : 0.004 0.047 5377 Dihedral : 4.680 26.661 4410 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3751 helix: 1.78 (0.21), residues: 673 sheet: -0.34 (0.16), residues: 1010 loop : -1.45 (0.13), residues: 2068 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 13 residues processed: 259 average time/residue: 0.4304 time to fit residues: 186.5206 Evaluate side-chains 224 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 3.624 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.3021 time to fit residues: 12.0860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 246 optimal weight: 0.0670 chunk 179 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 284 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 30889 Z= 0.159 Angle : 0.555 11.706 42040 Z= 0.282 Chirality : 0.045 0.630 4906 Planarity : 0.004 0.046 5377 Dihedral : 4.476 25.373 4410 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3751 helix: 1.99 (0.21), residues: 672 sheet: -0.19 (0.16), residues: 1046 loop : -1.33 (0.13), residues: 2033 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 244 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 262 average time/residue: 0.4379 time to fit residues: 191.8096 Evaluate side-chains 244 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 229 time to evaluate : 3.522 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2803 time to fit residues: 12.7300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 7.9990 chunk 347 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 337 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 319 optimal weight: 0.9980 chunk 336 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.108 30889 Z= 0.327 Angle : 0.614 11.665 42040 Z= 0.316 Chirality : 0.046 0.632 4906 Planarity : 0.004 0.061 5377 Dihedral : 4.701 25.829 4410 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3751 helix: 1.84 (0.21), residues: 668 sheet: -0.34 (0.16), residues: 1050 loop : -1.41 (0.13), residues: 2033 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 4.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 248 average time/residue: 0.4549 time to fit residues: 190.1870 Evaluate side-chains 227 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 4.551 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3074 time to fit residues: 11.4013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 3.9990 chunk 357 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 30889 Z= 0.220 Angle : 0.577 11.489 42040 Z= 0.297 Chirality : 0.046 0.765 4906 Planarity : 0.004 0.050 5377 Dihedral : 4.593 24.907 4410 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3751 helix: 1.89 (0.21), residues: 671 sheet: -0.24 (0.16), residues: 1049 loop : -1.40 (0.13), residues: 2031 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 232 average time/residue: 0.4347 time to fit residues: 169.2866 Evaluate side-chains 228 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 222 time to evaluate : 3.591 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3199 time to fit residues: 8.5484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 0.0870 chunk 298 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 306 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 804 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.108982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075546 restraints weight = 75403.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078182 restraints weight = 45332.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.079933 restraints weight = 32968.197| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 30889 Z= 0.162 Angle : 0.560 11.780 42040 Z= 0.285 Chirality : 0.045 0.774 4906 Planarity : 0.004 0.062 5377 Dihedral : 4.433 24.290 4410 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3751 helix: 2.03 (0.21), residues: 672 sheet: -0.11 (0.16), residues: 1052 loop : -1.35 (0.13), residues: 2027 =============================================================================== Job complete usr+sys time: 5963.67 seconds wall clock time: 110 minutes 49.70 seconds (6649.70 seconds total)