Starting phenix.real_space_refine on Wed Feb 21 23:31:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wec_32446/02_2024/7wec_32446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wec_32446/02_2024/7wec_32446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wec_32446/02_2024/7wec_32446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wec_32446/02_2024/7wec_32446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wec_32446/02_2024/7wec_32446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wec_32446/02_2024/7wec_32446.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 20471 2.51 5 N 5287 2.21 5 O 6318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 71": "OD1" <-> "OD2" Residue "K TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 985": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32217 Number of models: 1 Model: "" Number of chains: 33 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.46, per 1000 atoms: 0.51 Number of scatterers: 32217 At special positions: 0 Unit cell: (163.71, 164.78, 208.65, 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 141 16.00 O 6318 8.00 N 5287 7.00 C 20471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 107 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.04 Simple disulfide: pdb=" SG CYS I 102 " - pdb=" SG CYS I 107 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.05 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.05 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.02 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.05 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.02 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 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=12, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A1302 " - " ASN A1155 " " NAG A1303 " - " ASN A 143 " " NAG A1304 " - " ASN A 17 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 600 " " NAG A1308 " - " ASN A 654 " " NAG A1309 " - " ASN A 613 " " NAG A1310 " - " ASN A 706 " " NAG B1302 " - " ASN B1155 " " NAG B1303 " - " ASN B 123 " " NAG B1304 " - " ASN B 143 " " NAG B1305 " - " ASN B 17 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 600 " " NAG B1309 " - " ASN B 654 " " NAG B1310 " - " ASN B 613 " " NAG B1311 " - " ASN B 706 " " NAG C1301 " - " ASN C1155 " " NAG C1302 " - " ASN C 123 " " NAG C1303 " - " ASN C 143 " " NAG C1304 " - " ASN C 17 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 600 " " NAG C1308 " - " ASN C 654 " " NAG C1309 " - " ASN C 613 " " NAG C1310 " - " ASN C 706 " " NAG D 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 714 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN A 798 " " NAG O 1 " - " ASN A1095 " " NAG P 1 " - " ASN A1131 " " NAG S 1 " - " ASN B 714 " " NAG U 1 " - " ASN B 798 " " NAG V 1 " - " ASN B1095 " " NAG W 1 " - " ASN B1131 " " NAG X 1 " - " ASN C 231 " " NAG Z 1 " - " ASN C 714 " " NAG b 1 " - " ASN C 798 " " NAG c 1 " - " ASN C1095 " " NAG d 1 " - " ASN C1131 " Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.34 Conformation dependent library (CDL) restraints added in 5.9 seconds 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7464 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 69 sheets defined 20.3% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'H' and resid 63 through 66 removed outlier: 3.691A pdb=" N GLN H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 66' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.687A pdb=" N THR H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 341 removed outlier: 4.119A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.819A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 5.199A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.637A pdb=" N ILE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.734A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 777 removed outlier: 3.787A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 removed outlier: 3.589A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.738A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 878 removed outlier: 4.066A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.885A pdb=" N GLY A 886 " --> pdb=" O TRP A 883 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 887' Processing helix chain 'A' and resid 894 through 905 removed outlier: 4.046A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.980A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 936 removed outlier: 3.781A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 936 " --> pdb=" O GLN A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 4.016A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.823A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 979 " --> pdb=" O ASN A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 973 through 979' Processing helix chain 'A' and resid 985 through 1029 removed outlier: 3.827A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A1018 " --> pdb=" O GLU A1014 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A1024 " --> pdb=" O ASN A1020 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A1027 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1147 removed outlier: 3.695A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1158 removed outlier: 3.727A pdb=" N SER A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.195A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.150A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 4.686A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 735 through 740 removed outlier: 4.313A pdb=" N ILE B 739 " --> pdb=" O CYS B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 748 removed outlier: 3.715A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 743 through 748' Processing helix chain 'B' and resid 750 through 754 Processing helix chain 'B' and resid 755 through 777 removed outlier: 3.548A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 822 removed outlier: 3.632A pdb=" N LEU B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 851 removed outlier: 3.730A pdb=" N LYS B 851 " --> pdb=" O CYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 878 removed outlier: 3.525A pdb=" N SER B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 897 Processing helix chain 'B' and resid 898 through 905 Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.945A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 910 through 915' Processing helix chain 'B' and resid 916 through 936 removed outlier: 3.698A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 936 " --> pdb=" O GLN B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.987A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 956 " --> pdb=" O ASN B 952 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 959 " --> pdb=" O ALA B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 985 through 1016 removed outlier: 3.808A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1029 removed outlier: 3.951A pdb=" N THR B1024 " --> pdb=" O ASN B1020 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B1027 " --> pdb=" O ALA B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.982A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1158 removed outlier: 3.775A pdb=" N SER B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.207A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.663A pdb=" N ALA C 349 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP C 350 " --> pdb=" O VAL C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 350' Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 384 removed outlier: 4.085A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 4.925A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.895A pdb=" N TYR C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 620 removed outlier: 4.117A pdb=" N VAL C 619 " --> pdb=" O THR C 615 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 620' Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.747A pdb=" N TYR C 633 " --> pdb=" O TRP C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 removed outlier: 4.206A pdb=" N TYR C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE C 739 " --> pdb=" O CYS C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.518A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 757 through 779 removed outlier: 3.762A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 778 " --> pdb=" O ASN C 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 779 " --> pdb=" O THR C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 removed outlier: 3.630A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 removed outlier: 3.781A pdb=" N GLN C 850 " --> pdb=" O ILE C 847 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 851 " --> pdb=" O CYS C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 878 removed outlier: 4.271A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 870 " --> pdb=" O MET C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.950A pdb=" N GLY C 886 " --> pdb=" O TRP C 883 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 883 through 887' Processing helix chain 'C' and resid 894 through 905 removed outlier: 4.160A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 902 " --> pdb=" O GLN C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 4.047A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 916 " --> pdb=" O VAL C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 removed outlier: 3.770A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 936 " --> pdb=" O GLN C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 4.038A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.553A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 979 " --> pdb=" O ASN C 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 973 through 979' Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.736A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C1017 " --> pdb=" O ALA C1013 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR C1024 " --> pdb=" O ASN C1020 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.199A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1158 removed outlier: 3.873A pdb=" N SER C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.889A pdb=" N CYS G 22 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.327A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 35 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG G 39 " --> pdb=" O TRP G 48 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TRP G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.799A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS H 22 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA H 80 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.379A pdb=" N GLU H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU H 35 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.300A pdb=" N GLU I 10 " --> pdb=" O THR I 121 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU I 35 " --> pdb=" O TRP I 51 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP I 51 " --> pdb=" O LEU I 35 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU I 47 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.300A pdb=" N GLU I 10 " --> pdb=" O THR I 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA I 99 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 113 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 17 through 21 Processing sheet with id=AA8, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.577A pdb=" N THR J 73 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.834A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN J 39 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.737A pdb=" N THR K 73 " --> pdb=" O SER K 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.010A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL K 86 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER K 54 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.708A pdb=" N THR L 73 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.854A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.567A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 261 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N HIS A 202 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N LEU A 220 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.943A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AB8, first strand: chain 'A' and resid 308 through 312 removed outlier: 4.737A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 609 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 646 " --> pdb=" O TYR A 609 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 321 through 322 removed outlier: 7.366A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.633A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AC3, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.653A pdb=" N TYR A 470 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.661A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 548 through 551 removed outlier: 5.384A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.747A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 698 through 699 removed outlier: 7.156A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AC9, first strand: chain 'A' and resid 715 through 725 removed outlier: 6.911A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.562A pdb=" N ALA A1053 " --> pdb=" O GLY A1056 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AD3, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 3.602A pdb=" N SER A1120 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AD5, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.620A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 261 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 198 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 224 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.946A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 99 through 104 removed outlier: 6.395A pdb=" N LEU B 238 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TRP B 102 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN B 236 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AD9, first strand: chain 'B' and resid 113 through 114 removed outlier: 6.413A pdb=" N ILE B 126 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 164 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 128 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 308 through 315 removed outlier: 4.702A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 321 through 322 removed outlier: 7.480A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.762A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 399 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLY B 428 " --> pdb=" O CYS B 376 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N CYS B 376 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 430 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B 374 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 432 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.267A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AE6, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AE7, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.743A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.503A pdb=" N ASP B 583 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.024A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AF2, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.523A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 715 through 725 Processing sheet with id=AF4, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AF5, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 3.554A pdb=" N SER B1120 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AF7, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.697A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N HIS C 202 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N LEU C 220 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.905A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AG1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AG2, first strand: chain 'C' and resid 315 through 316 Processing sheet with id=AG3, first strand: chain 'C' and resid 321 through 322 removed outlier: 7.433A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.871A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 394 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 355 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 358 through 359 removed outlier: 7.449A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'C' and resid 449 through 451 removed outlier: 3.501A pdb=" N TYR C 450 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 490 " --> pdb=" O TYR C 450 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AG8, first strand: chain 'C' and resid 539 through 540 Processing sheet with id=AG9, first strand: chain 'C' and resid 548 through 551 Processing sheet with id=AH1, first strand: chain 'C' and resid 562 through 564 removed outlier: 4.137A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 651 through 657 removed outlier: 5.894A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.748A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.543A pdb=" N ALA C1053 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 732 through 733 Processing sheet with id=AH6, first strand: chain 'C' and resid 1078 through 1079 removed outlier: 4.912A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.04 Time building geometry restraints manager: 14.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5156 1.31 - 1.44: 9396 1.44 - 1.58: 18220 1.58 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 32949 Sorted by residual: bond pdb=" C PRO C 576 " pdb=" O PRO C 576 " ideal model delta sigma weight residual 1.235 1.180 0.056 1.30e-02 5.92e+03 1.82e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N PHE A 326 " pdb=" CA PHE A 326 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.56e+01 bond pdb=" C PRO B 576 " pdb=" O PRO B 576 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.19e+01 bond pdb=" N VAL A 305 " pdb=" CA VAL A 305 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.28e-02 6.10e+03 1.06e+01 ... (remaining 32944 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.53: 404 103.53 - 111.22: 13678 111.22 - 118.92: 12832 118.92 - 126.62: 17493 126.62 - 134.32: 405 Bond angle restraints: 44812 Sorted by residual: angle pdb=" N LEU C 139 " pdb=" CA LEU C 139 " pdb=" C LEU C 139 " ideal model delta sigma weight residual 112.92 99.54 13.38 1.23e+00 6.61e-01 1.18e+02 angle pdb=" C GLU B 211 " pdb=" CA GLU B 211 " pdb=" CB GLU B 211 " ideal model delta sigma weight residual 116.54 110.21 6.33 1.15e+00 7.56e-01 3.03e+01 angle pdb=" N ASP C 140 " pdb=" CA ASP C 140 " pdb=" C ASP C 140 " ideal model delta sigma weight residual 111.07 116.72 -5.65 1.07e+00 8.73e-01 2.79e+01 angle pdb=" N LEU B 139 " pdb=" CA LEU B 139 " pdb=" C LEU B 139 " ideal model delta sigma weight residual 113.17 106.59 6.58 1.26e+00 6.30e-01 2.72e+01 angle pdb=" N GLN B 577 " pdb=" CA GLN B 577 " pdb=" C GLN B 577 " ideal model delta sigma weight residual 113.43 106.87 6.56 1.26e+00 6.30e-01 2.71e+01 ... (remaining 44807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 19208 23.07 - 46.13: 1201 46.13 - 69.20: 156 69.20 - 92.26: 61 92.26 - 115.33: 31 Dihedral angle restraints: 20657 sinusoidal: 9059 harmonic: 11598 Sorted by residual: dihedral pdb=" CA SER J 95 " pdb=" C SER J 95 " pdb=" N PRO J 96 " pdb=" CA PRO J 96 " ideal model delta harmonic sigma weight residual -180.00 -141.06 -38.94 0 5.00e+00 4.00e-02 6.07e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 97 " pdb=" CB CYS G 97 " ideal model delta sinusoidal sigma weight residual 93.00 146.26 -53.26 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA CYS A 161 " pdb=" C CYS A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -149.45 -30.55 0 5.00e+00 4.00e-02 3.73e+01 ... (remaining 20654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 5228 0.156 - 0.311: 37 0.311 - 0.467: 3 0.467 - 0.622: 0 0.622 - 0.778: 1 Chirality restraints: 5269 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 123 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CA HIS C 141 " pdb=" N HIS C 141 " pdb=" C HIS C 141 " pdb=" CB HIS C 141 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA LEU C 139 " pdb=" N LEU C 139 " pdb=" C LEU C 139 " pdb=" CB LEU C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 5266 not shown) Planarity restraints: 5709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 336 " -0.023 2.00e-02 2.50e+03 4.83e-02 2.34e+01 pdb=" CG ASP B 336 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASP B 336 " -0.031 2.00e-02 2.50e+03 pdb=" OD2 ASP B 336 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " 0.014 2.00e-02 2.50e+03 3.86e-02 1.86e+01 pdb=" C7 NAG B1306 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.004 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " 0.065 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO L 96 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.054 5.00e-02 4.00e+02 ... (remaining 5706 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 97 2.41 - 3.03: 18949 3.03 - 3.65: 45387 3.65 - 4.28: 66571 4.28 - 4.90: 113306 Nonbonded interactions: 244310 Sorted by model distance: nonbonded pdb=" OD2 ASP B 336 " pdb=" O7 NAG B1306 " model vdw 1.785 2.432 nonbonded pdb=" OD1 ASP B 336 " pdb=" N2 NAG B1306 " model vdw 2.012 2.496 nonbonded pdb=" OD1 ASP B 336 " pdb=" C8 NAG B1306 " model vdw 2.095 2.768 nonbonded pdb=" OH TYR B 633 " pdb=" O ILE B 648 " model vdw 2.121 2.440 nonbonded pdb=" O PRO B 460 " pdb=" O3 NAG B1301 " model vdw 2.157 2.440 ... (remaining 244305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 1159 or resid 1301 through 1310)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'W' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.520 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 87.420 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 32949 Z= 0.328 Angle : 0.735 13.380 44812 Z= 0.389 Chirality : 0.052 0.778 5269 Planarity : 0.005 0.098 5668 Dihedral : 15.351 115.331 13049 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.65 % Favored : 93.23 % Rotamer: Outliers : 0.26 % Allowed : 0.69 % Favored : 99.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.51 % Twisted General : 0.03 % 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: -1.96 (0.13), residues: 3942 helix: -2.31 (0.17), residues: 704 sheet: -0.00 (0.17), residues: 979 loop : -1.58 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 51 HIS 0.005 0.001 HIS C 141 PHE 0.022 0.001 PHE C 196 TYR 0.018 0.001 TYR C 450 ARG 0.009 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 264 time to evaluate : 3.528 Fit side-chains revert: symmetry clash REVERT: H 112 ASP cc_start: 0.7566 (m-30) cc_final: 0.7297 (m-30) REVERT: K 92 TYR cc_start: 0.7520 (m-10) cc_final: 0.7300 (m-80) REVERT: A 357 ASN cc_start: 0.8047 (m-40) cc_final: 0.7765 (t0) REVERT: A 777 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 386 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7408 (p0) REVERT: B 777 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7564 (mt-10) REVERT: C 255 TRP cc_start: 0.3711 (OUTLIER) cc_final: 0.3193 (p-90) outliers start: 9 outliers final: 1 residues processed: 270 average time/residue: 0.4605 time to fit residues: 199.2451 Evaluate side-chains 212 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 329 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 0.0170 chunk 297 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 759 GLN A1139 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 52 GLN C 85 ASN C1116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 32949 Z= 0.319 Angle : 0.676 19.251 44812 Z= 0.338 Chirality : 0.049 0.489 5269 Planarity : 0.005 0.063 5668 Dihedral : 9.851 103.946 5918 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.13 % Rotamer: Outliers : 0.78 % Allowed : 9.37 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.51 % 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: -1.78 (0.13), residues: 3942 helix: -1.54 (0.18), residues: 715 sheet: -0.07 (0.17), residues: 1007 loop : -1.61 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.011 0.001 HIS C 202 PHE 0.026 0.002 PHE G 101 TYR 0.026 0.002 TYR A 393 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 112 ASP cc_start: 0.7571 (m-30) cc_final: 0.7325 (m-30) REVERT: K 39 GLN cc_start: 0.7184 (tt0) cc_final: 0.6878 (tp40) REVERT: B 139 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7284 (tt) REVERT: B 386 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7443 (p0) REVERT: B 777 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7728 (mt-10) outliers start: 27 outliers final: 23 residues processed: 233 average time/residue: 0.4462 time to fit residues: 167.1729 Evaluate side-chains 227 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 51 TRP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 351 ASN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 243 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 386 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 354 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN A 999 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32949 Z= 0.255 Angle : 0.620 19.043 44812 Z= 0.308 Chirality : 0.047 0.464 5269 Planarity : 0.004 0.068 5668 Dihedral : 8.314 102.218 5918 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.04 % Rotamer: Outliers : 1.99 % Allowed : 11.59 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.51 % 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: -1.71 (0.13), residues: 3942 helix: -1.27 (0.19), residues: 727 sheet: -0.05 (0.17), residues: 1014 loop : -1.64 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.010 0.001 HIS C 202 PHE 0.019 0.001 PHE B1118 TYR 0.018 0.001 TYR C1064 ARG 0.006 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 214 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 112 ASP cc_start: 0.7526 (m-30) cc_final: 0.7297 (m-30) REVERT: K 39 GLN cc_start: 0.7303 (tt0) cc_final: 0.6987 (tp40) REVERT: K 92 TYR cc_start: 0.7646 (m-80) cc_final: 0.7356 (m-80) REVERT: B 139 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7428 (tp) REVERT: B 777 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7751 (mt-10) REVERT: C 41 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8522 (mtpp) outliers start: 69 outliers final: 42 residues processed: 267 average time/residue: 0.4289 time to fit residues: 189.0112 Evaluate side-chains 251 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 351 ASN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 585 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 358 optimal weight: 0.0980 chunk 379 optimal weight: 0.1980 chunk 187 optimal weight: 7.9990 chunk 340 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32949 Z= 0.189 Angle : 0.595 19.389 44812 Z= 0.292 Chirality : 0.045 0.474 5269 Planarity : 0.004 0.065 5668 Dihedral : 7.583 103.094 5916 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 2.28 % Allowed : 13.64 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.51 % 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: -1.56 (0.13), residues: 3942 helix: -1.00 (0.19), residues: 727 sheet: 0.04 (0.16), residues: 1011 loop : -1.60 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.008 0.001 HIS C 202 PHE 0.023 0.001 PHE B 756 TYR 0.016 0.001 TYR B 498 ARG 0.004 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 217 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6682 (mmmm) cc_final: 0.5581 (mptt) REVERT: H 112 ASP cc_start: 0.7523 (m-30) cc_final: 0.7307 (m-30) REVERT: K 39 GLN cc_start: 0.7259 (tt0) cc_final: 0.6956 (tp40) REVERT: K 92 TYR cc_start: 0.7648 (m-80) cc_final: 0.7408 (m-80) REVERT: A 549 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8606 (mt) REVERT: B 139 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7427 (tp) REVERT: C 41 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8512 (mtpp) outliers start: 79 outliers final: 52 residues processed: 280 average time/residue: 0.4243 time to fit residues: 195.1186 Evaluate side-chains 255 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 200 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 351 ASN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 262 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 193 optimal weight: 0.9980 chunk 340 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN A 850 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32949 Z= 0.244 Angle : 0.612 19.411 44812 Z= 0.301 Chirality : 0.046 0.475 5269 Planarity : 0.004 0.071 5668 Dihedral : 7.401 103.819 5916 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.42 % Favored : 93.53 % Rotamer: Outliers : 2.80 % Allowed : 14.79 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.58 (0.13), residues: 3942 helix: -0.91 (0.19), residues: 731 sheet: -0.02 (0.16), residues: 1013 loop : -1.62 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.004 0.001 HIS C 141 PHE 0.019 0.001 PHE C 196 TYR 0.017 0.001 TYR C1064 ARG 0.006 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 207 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6693 (mmmm) cc_final: 0.5535 (mptt) REVERT: H 112 ASP cc_start: 0.7400 (m-30) cc_final: 0.7199 (m-30) REVERT: I 36 GLN cc_start: 0.7196 (pt0) cc_final: 0.6583 (pt0) REVERT: K 39 GLN cc_start: 0.7233 (tt0) cc_final: 0.6992 (tp40) REVERT: B 139 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7417 (tp) REVERT: C 41 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8428 (mtpp) outliers start: 97 outliers final: 70 residues processed: 287 average time/residue: 0.4189 time to fit residues: 199.1360 Evaluate side-chains 274 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 202 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 351 ASN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 998 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 0.7980 chunk 342 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 380 optimal weight: 0.8980 chunk 315 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B 952 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 32949 Z= 0.403 Angle : 0.696 19.471 44812 Z= 0.345 Chirality : 0.049 0.481 5269 Planarity : 0.004 0.070 5668 Dihedral : 7.564 103.565 5914 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.53 % Favored : 92.42 % Rotamer: Outliers : 3.37 % Allowed : 15.28 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.75 (0.13), residues: 3942 helix: -1.09 (0.18), residues: 736 sheet: -0.09 (0.17), residues: 982 loop : -1.73 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.006 0.001 HIS C1061 PHE 0.031 0.002 PHE C1118 TYR 0.019 0.002 TYR C1064 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 214 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6443 (mmmm) cc_final: 0.5406 (mptt) REVERT: H 112 ASP cc_start: 0.7342 (m-30) cc_final: 0.7138 (m-30) REVERT: I 36 GLN cc_start: 0.7232 (pt0) cc_final: 0.6606 (pt0) REVERT: K 39 GLN cc_start: 0.7255 (tt0) cc_final: 0.7019 (tp40) REVERT: A 549 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8654 (mt) REVERT: B 386 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7462 (p0) REVERT: C 41 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8903 (mttp) REVERT: C 82 LEU cc_start: 0.1846 (OUTLIER) cc_final: 0.1540 (pp) outliers start: 117 outliers final: 86 residues processed: 317 average time/residue: 0.4327 time to fit residues: 226.4798 Evaluate side-chains 296 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 206 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 1.9990 chunk 42 optimal weight: 40.0000 chunk 216 optimal weight: 0.5980 chunk 277 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 320 optimal weight: 0.9990 chunk 212 optimal weight: 0.0000 chunk 378 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32949 Z= 0.166 Angle : 0.602 19.582 44812 Z= 0.294 Chirality : 0.045 0.480 5269 Planarity : 0.004 0.075 5668 Dihedral : 7.042 103.520 5914 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 2.54 % Allowed : 16.67 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.51 (0.13), residues: 3942 helix: -0.73 (0.19), residues: 728 sheet: 0.05 (0.17), residues: 963 loop : -1.61 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 48 HIS 0.004 0.001 HIS C 141 PHE 0.017 0.001 PHE C 196 TYR 0.016 0.001 TYR A1064 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 213 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6357 (mmmm) cc_final: 0.5329 (mptt) REVERT: A 549 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8638 (mt) REVERT: A 749 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8621 (mp) REVERT: A 883 TRP cc_start: 0.8272 (p90) cc_final: 0.8069 (p90) REVERT: B 139 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7462 (tp) REVERT: B 172 MET cc_start: 0.3881 (mmm) cc_final: 0.3464 (mpp) REVERT: B 354 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7730 (ttm-80) REVERT: C 41 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8379 (mtpp) REVERT: C 723 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8626 (mt) outliers start: 88 outliers final: 66 residues processed: 286 average time/residue: 0.4419 time to fit residues: 205.3167 Evaluate side-chains 273 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 202 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1098 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 0.0170 chunk 151 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 297 optimal weight: 6.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32949 Z= 0.355 Angle : 0.678 19.465 44812 Z= 0.334 Chirality : 0.048 0.483 5269 Planarity : 0.004 0.074 5668 Dihedral : 7.210 104.491 5914 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.56 % Favored : 92.36 % Rotamer: Outliers : 3.34 % Allowed : 16.44 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.68 (0.13), residues: 3942 helix: -0.94 (0.19), residues: 737 sheet: -0.07 (0.17), residues: 980 loop : -1.70 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.004 0.001 HIS B 516 PHE 0.028 0.002 PHE C1118 TYR 0.019 0.001 TYR C1064 ARG 0.006 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 212 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6392 (mmmm) cc_final: 0.5380 (mptt) REVERT: A 188 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 549 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8618 (mt) REVERT: A 749 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8816 (tt) REVERT: B 354 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7744 (ttm-80) REVERT: B 483 PHE cc_start: 0.8303 (t80) cc_final: 0.8102 (t80) REVERT: C 41 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8900 (mttp) REVERT: C 874 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8658 (mm) outliers start: 116 outliers final: 93 residues processed: 308 average time/residue: 0.4225 time to fit residues: 212.4150 Evaluate side-chains 304 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 206 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1098 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 8.9990 chunk 362 optimal weight: 0.2980 chunk 331 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 chunk 212 optimal weight: 0.0970 chunk 153 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 318 optimal weight: 0.1980 chunk 333 optimal weight: 7.9990 chunk 351 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32949 Z= 0.164 Angle : 0.603 19.639 44812 Z= 0.295 Chirality : 0.045 0.481 5269 Planarity : 0.004 0.073 5668 Dihedral : 6.751 105.258 5914 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.22 % Rotamer: Outliers : 2.74 % Allowed : 17.27 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.49 (0.13), residues: 3942 helix: -0.65 (0.19), residues: 730 sheet: -0.00 (0.17), residues: 985 loop : -1.61 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 48 HIS 0.003 0.001 HIS C 141 PHE 0.019 0.001 PHE C 196 TYR 0.016 0.001 TYR A1064 ARG 0.006 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 209 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6323 (mmmm) cc_final: 0.5254 (mptt) REVERT: J 24 ARG cc_start: 0.8061 (tpp-160) cc_final: 0.7817 (mmp80) REVERT: A 549 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8638 (mt) REVERT: A 749 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8643 (mp) REVERT: B 139 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7399 (tp) REVERT: B 483 PHE cc_start: 0.8281 (t80) cc_final: 0.8079 (t80) REVERT: C 41 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8373 (mtpp) REVERT: C 452 LEU cc_start: 0.8594 (mm) cc_final: 0.8142 (mm) REVERT: C 723 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8623 (mt) REVERT: C 874 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8647 (mm) outliers start: 95 outliers final: 83 residues processed: 290 average time/residue: 0.4285 time to fit residues: 204.2398 Evaluate side-chains 295 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 206 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1098 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 0.9990 chunk 373 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 391 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 311 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32949 Z= 0.338 Angle : 0.670 19.516 44812 Z= 0.331 Chirality : 0.048 0.481 5269 Planarity : 0.004 0.078 5668 Dihedral : 6.992 105.489 5914 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 2.94 % Allowed : 16.98 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.64 (0.13), residues: 3942 helix: -0.87 (0.19), residues: 737 sheet: -0.08 (0.17), residues: 988 loop : -1.68 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 64 HIS 0.004 0.001 HIS B 516 PHE 0.030 0.002 PHE C 196 TYR 0.018 0.001 TYR C1064 ARG 0.008 0.000 ARG B 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 205 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6366 (mmmm) cc_final: 0.5318 (mptt) REVERT: A 188 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (t) REVERT: A 549 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8618 (mt) REVERT: B 386 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7451 (p0) REVERT: B 483 PHE cc_start: 0.8287 (t80) cc_final: 0.8056 (t80) REVERT: C 874 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8641 (mm) outliers start: 102 outliers final: 92 residues processed: 291 average time/residue: 0.4173 time to fit residues: 200.7198 Evaluate side-chains 300 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 204 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 287 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 312 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 320 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 1 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.149723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095338 restraints weight = 60794.714| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.38 r_work: 0.3220 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32949 Z= 0.197 Angle : 0.613 19.669 44812 Z= 0.300 Chirality : 0.045 0.482 5269 Planarity : 0.004 0.069 5668 Dihedral : 6.737 105.475 5914 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 2.83 % Allowed : 17.27 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.52 (0.13), residues: 3942 helix: -0.69 (0.19), residues: 730 sheet: 0.01 (0.16), residues: 1001 loop : -1.64 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 48 HIS 0.003 0.001 HIS C1098 PHE 0.026 0.001 PHE H 101 TYR 0.016 0.001 TYR C1064 ARG 0.007 0.000 ARG B 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6248.02 seconds wall clock time: 115 minutes 41.83 seconds (6941.83 seconds total)