Starting phenix.real_space_refine on Thu Mar 21 13:11:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h01_34408/03_2024/8h01_34408.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h01_34408/03_2024/8h01_34408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h01_34408/03_2024/8h01_34408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h01_34408/03_2024/8h01_34408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h01_34408/03_2024/8h01_34408.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h01_34408/03_2024/8h01_34408.pdb" } resolution = 3.7 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= -0.001 sd= 0.037 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 19224 2.51 5 N 4932 2.21 5 O 5847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 96": "OD1" <-> "OD2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 33": "OD1" <-> "OD2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30144 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8118 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 976} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8119 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8113 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 15.30, per 1000 atoms: 0.51 Number of scatterers: 30144 At special positions: 0 Unit cell: (147.264, 162.24, 198.016, 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 5847 8.00 N 4932 7.00 C 19224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 50 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 50 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 50 " 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=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1074 " " NAG W 1 " - " ASN A1098 " " NAG X 1 " - " ASN A1134 " Time building additional restraints: 12.05 Conformation dependent library (CDL) restraints added in 4.9 seconds 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7078 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 69 sheets defined 20.7% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.585A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.569A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 387' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.151A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.973A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.054A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.085A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.497A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.240A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.380A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.543A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.613A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.023A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.966A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.613A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.098A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.180A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.499A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.923A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.562A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.553A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.450A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.542A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.596A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.690A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.092A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.524A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.500A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 removed outlier: 3.847A pdb=" N LYS E 66 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.716A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.068A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 52 No H-bonds generated for 'chain 'H' and resid 50 through 52' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.861A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.893A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.896A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.760A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.549A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 6.364A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.091A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.504A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.504A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.320A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.902A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.919A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 7.245A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.365A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.333A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.656A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.776A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.134A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.313A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.136A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.778A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.164A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.015A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.758A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.758A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.517A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.786A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.676A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.790A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.391A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.303A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.601A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.675A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.108A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.780A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.695A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.695A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.072A pdb=" N VAL D 11 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 105 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.697A pdb=" N THR E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.739A pdb=" N ASP E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.781A pdb=" N LEU E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.587A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.407A pdb=" N VAL F 11 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS F 110 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU F 13 " --> pdb=" O LYS F 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.590A pdb=" N THR F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 48 through 49 Processing sheet with id=AG6, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.522A pdb=" N LEU G 17 " --> pdb=" O MET G 83 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET G 83 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.810A pdb=" N ILE G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N CYS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N MET G 34 " --> pdb=" O CYS G 50 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP G 33 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.810A pdb=" N ILE G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N CYS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N MET G 34 " --> pdb=" O CYS G 50 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP G 33 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.586A pdb=" N THR H 7 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 10 through 14 removed outlier: 6.430A pdb=" N VAL H 11 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS H 110 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU H 13 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 105 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 48 through 49 Processing sheet with id=AH3, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.670A pdb=" N MET I 83 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR I 78 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.677A pdb=" N LEU I 111 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AH6, first strand: chain 'I' and resid 49 through 50 1189 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.28 Time building geometry restraints manager: 12.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9492 1.34 - 1.46: 6766 1.46 - 1.58: 14405 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 30840 Sorted by residual: bond pdb=" N ILE D 29 " pdb=" CA ILE D 29 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.38e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.25e-02 6.40e+03 8.84e+00 bond pdb=" N LYS F 45 " pdb=" CA LYS F 45 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.21e-02 6.83e+03 7.70e+00 bond pdb=" N ASP G 33 " pdb=" CA ASP G 33 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.66e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.43e+00 ... (remaining 30835 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.57: 664 105.57 - 112.75: 16564 112.75 - 119.92: 9978 119.92 - 127.10: 14459 127.10 - 134.27: 301 Bond angle restraints: 41966 Sorted by residual: angle pdb=" N GLY F 41 " pdb=" CA GLY F 41 " pdb=" C GLY F 41 " ideal model delta sigma weight residual 115.36 110.14 5.22 1.33e+00 5.65e-01 1.54e+01 angle pdb=" N ILE D 29 " pdb=" CA ILE D 29 " pdb=" C ILE D 29 " ideal model delta sigma weight residual 112.43 108.83 3.60 9.20e-01 1.18e+00 1.53e+01 angle pdb=" N GLY A 857 " pdb=" CA GLY A 857 " pdb=" C GLY A 857 " ideal model delta sigma weight residual 115.27 110.10 5.17 1.41e+00 5.03e-01 1.35e+01 angle pdb=" CA ASN C 331 " pdb=" C ASN C 331 " pdb=" O ASN C 331 " ideal model delta sigma weight residual 122.64 118.21 4.43 1.25e+00 6.40e-01 1.26e+01 angle pdb=" CA ASN B 331 " pdb=" C ASN B 331 " pdb=" O ASN B 331 " ideal model delta sigma weight residual 122.41 118.19 4.22 1.21e+00 6.83e-01 1.22e+01 ... (remaining 41961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 17253 18.00 - 35.99: 1323 35.99 - 53.99: 246 53.99 - 71.99: 51 71.99 - 89.99: 34 Dihedral angle restraints: 18907 sinusoidal: 7888 harmonic: 11019 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.52 -75.48 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.07 -60.93 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 34.80 58.20 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 18904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 4876 0.307 - 0.613: 1 0.613 - 0.920: 0 0.920 - 1.227: 0 1.227 - 1.534: 1 Chirality restraints: 4878 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.88e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4875 not shown) Planarity restraints: 5376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.041 2.00e-02 2.50e+03 9.43e-02 1.11e+02 pdb=" CG ASN C 331 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.169 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO C 986 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.000 2.00e-02 2.50e+03 1.97e-02 4.87e+00 pdb=" CG ASN B 234 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.025 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.021 2.00e-02 2.50e+03 ... (remaining 5373 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2627 2.74 - 3.28: 30316 3.28 - 3.82: 49863 3.82 - 4.36: 57334 4.36 - 4.90: 100558 Nonbonded interactions: 240698 Sorted by model distance: nonbonded pdb=" OG SER A 247 " pdb=" OG1 THR A 259 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR I 80 " pdb=" OE1 GLN I 82 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR B 124 " pdb=" OD1 ASN B 125 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.243 2.440 ... (remaining 240693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 356 or (resid 357 and (name N or name CA or nam \ e C or name O or name CB )) or resid 358 through 579 or (resid 580 and (name N o \ r name CA or name C or name O or name CB )) or resid 581 through 977 or (resid 9 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 979 through \ 993 or (resid 994 and (name N or name CA or name C or name O or name CB )) or r \ esid 995 through 1147 or resid 1301 through 1304)) selection = (chain 'B' and (resid 15 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 356 or (resid 357 and (name N or n \ ame CA or name C or name O or name CB )) or resid 358 through 827 or resid 853 t \ hrough 977 or (resid 978 and (name N or name CA or name C or name O or name CB ) \ ) or resid 979 through 1147 or resid 1301 through 1304)) selection = (chain 'C' and (resid 15 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 827 or resid 853 through 993 or (r \ esid 994 and (name N or name CA or name C or name O or name CB )) or resid 995 t \ hrough 1147 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.480 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: 0.040 Extract box with map and model: 28.430 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 81.670 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.004 0.041 30840 Z= 0.244 Angle : 0.570 7.757 41966 Z= 0.309 Chirality : 0.050 1.534 4878 Planarity : 0.004 0.058 5347 Dihedral : 13.235 89.985 11676 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3737 helix: 2.05 (0.21), residues: 659 sheet: 0.41 (0.18), residues: 867 loop : -0.94 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 112 HIS 0.003 0.001 HIS C 954 PHE 0.035 0.001 PHE A 906 TYR 0.014 0.001 TYR C 396 ARG 0.005 0.000 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 3.174 Fit side-chains REVERT: A 377 PHE cc_start: 0.8722 (p90) cc_final: 0.8402 (p90) REVERT: A 456 PHE cc_start: 0.8695 (m-80) cc_final: 0.8237 (m-80) REVERT: A 1050 MET cc_start: 0.8740 (ptt) cc_final: 0.8526 (ptt) REVERT: B 1005 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8152 (tm-30) REVERT: F 43 PRO cc_start: 0.6275 (Cg_exo) cc_final: 0.6037 (Cg_endo) REVERT: H 4 MET cc_start: 0.4318 (ttm) cc_final: 0.3966 (ttm) REVERT: I 34 MET cc_start: 0.2958 (tmm) cc_final: 0.2670 (ppp) REVERT: I 98 ARG cc_start: 0.7922 (tpt170) cc_final: 0.7362 (tpp80) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.4448 time to fit residues: 81.5723 Evaluate side-chains 86 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 343 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN F 76 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30840 Z= 0.227 Angle : 0.529 7.702 41966 Z= 0.279 Chirality : 0.043 0.265 4878 Planarity : 0.004 0.047 5347 Dihedral : 6.394 57.160 4990 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 0.30 % Allowed : 3.87 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3737 helix: 2.11 (0.21), residues: 679 sheet: 0.42 (0.18), residues: 871 loop : -0.87 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 32 HIS 0.003 0.001 HIS A1088 PHE 0.031 0.001 PHE A 338 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 3.457 Fit side-chains revert: symmetry clash REVERT: A 377 PHE cc_start: 0.8639 (p90) cc_final: 0.8423 (p90) REVERT: A 456 PHE cc_start: 0.8697 (m-80) cc_final: 0.8255 (m-80) REVERT: A 1050 MET cc_start: 0.8805 (ptt) cc_final: 0.8563 (ptt) REVERT: B 582 LEU cc_start: 0.9202 (mm) cc_final: 0.8908 (tp) REVERT: B 1005 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8156 (tm-30) REVERT: C 115 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7551 (tp40) REVERT: D 4 MET cc_start: 0.7145 (mpp) cc_final: 0.6479 (ptp) REVERT: H 4 MET cc_start: 0.4156 (ttm) cc_final: 0.3816 (ttm) REVERT: I 34 MET cc_start: 0.2965 (tmm) cc_final: 0.2720 (ppp) REVERT: I 98 ARG cc_start: 0.8005 (tpt170) cc_final: 0.7524 (tpp80) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.4264 time to fit residues: 67.7640 Evaluate side-chains 92 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 343 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 306 optimal weight: 0.4980 chunk 341 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 275 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN H 37 GLN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 30840 Z= 0.304 Angle : 0.539 7.298 41966 Z= 0.281 Chirality : 0.043 0.268 4878 Planarity : 0.004 0.043 5347 Dihedral : 6.115 58.314 4990 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 0.58 % Allowed : 6.59 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3737 helix: 2.00 (0.21), residues: 678 sheet: 0.27 (0.17), residues: 917 loop : -0.93 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 112 HIS 0.003 0.001 HIS A1088 PHE 0.020 0.001 PHE A 338 TYR 0.020 0.001 TYR B1067 ARG 0.008 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 3.761 Fit side-chains revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8727 (m-80) cc_final: 0.8295 (m-80) REVERT: A 1050 MET cc_start: 0.8851 (ptt) cc_final: 0.8574 (ptt) REVERT: B 582 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8921 (tp) REVERT: B 1005 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8181 (tm-30) REVERT: D 4 MET cc_start: 0.7161 (mpp) cc_final: 0.6674 (ptp) REVERT: H 4 MET cc_start: 0.4138 (ttm) cc_final: 0.3731 (ttm) REVERT: I 34 MET cc_start: 0.2907 (tmm) cc_final: 0.2561 (ppp) outliers start: 19 outliers final: 14 residues processed: 100 average time/residue: 0.4216 time to fit residues: 71.4542 Evaluate side-chains 96 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 chunk 178 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 230 optimal weight: 0.6980 chunk 345 optimal weight: 30.0000 chunk 365 optimal weight: 50.0000 chunk 180 optimal weight: 3.9990 chunk 327 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30840 Z= 0.252 Angle : 0.512 9.079 41966 Z= 0.267 Chirality : 0.043 0.269 4878 Planarity : 0.004 0.042 5347 Dihedral : 5.821 58.473 4990 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 0.73 % Allowed : 8.48 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3737 helix: 2.12 (0.21), residues: 673 sheet: 0.31 (0.17), residues: 915 loop : -0.92 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 112 HIS 0.003 0.001 HIS A1088 PHE 0.017 0.001 PHE A 338 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8738 (m-80) cc_final: 0.8313 (m-80) REVERT: A 1050 MET cc_start: 0.8849 (ptt) cc_final: 0.8576 (ptt) REVERT: B 582 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8919 (tp) REVERT: B 1005 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8156 (tm-30) REVERT: C 115 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7804 (tp40) REVERT: C 985 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8540 (m-30) REVERT: D 2 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7226 (mp) REVERT: H 24 GLN cc_start: 0.8834 (tt0) cc_final: 0.8406 (tm-30) REVERT: I 34 MET cc_start: 0.2902 (tmm) cc_final: 0.2615 (ppp) outliers start: 24 outliers final: 12 residues processed: 111 average time/residue: 0.4437 time to fit residues: 83.6127 Evaluate side-chains 97 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 252 optimal weight: 0.0270 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 327 optimal weight: 8.9990 chunk 92 optimal weight: 0.0570 overall best weight: 2.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C1083 HIS F 76 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30840 Z= 0.299 Angle : 0.534 7.754 41966 Z= 0.276 Chirality : 0.043 0.276 4878 Planarity : 0.004 0.042 5347 Dihedral : 5.704 58.329 4990 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 0.98 % Allowed : 9.73 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3737 helix: 2.08 (0.21), residues: 673 sheet: 0.19 (0.17), residues: 909 loop : -0.94 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 112 HIS 0.004 0.001 HIS C 519 PHE 0.016 0.001 PHE A 374 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8752 (m-80) cc_final: 0.8334 (m-80) REVERT: A 1050 MET cc_start: 0.8842 (ptt) cc_final: 0.8564 (ptt) REVERT: B 582 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8916 (tp) REVERT: B 1005 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 115 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7506 (tp40) REVERT: C 985 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: D 4 MET cc_start: 0.6604 (ptp) cc_final: 0.6101 (ptp) REVERT: H 24 GLN cc_start: 0.8802 (tt0) cc_final: 0.8400 (tm-30) REVERT: I 34 MET cc_start: 0.2830 (tmm) cc_final: 0.2513 (ppp) outliers start: 32 outliers final: 21 residues processed: 117 average time/residue: 0.3978 time to fit residues: 79.1242 Evaluate side-chains 106 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 72 optimal weight: 0.4980 chunk 214 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 365 optimal weight: 30.0000 chunk 303 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 804 GLN C 935 GLN D 90 GLN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30840 Z= 0.202 Angle : 0.499 7.934 41966 Z= 0.258 Chirality : 0.043 0.274 4878 Planarity : 0.004 0.044 5347 Dihedral : 5.432 57.461 4990 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 0.95 % Allowed : 10.67 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3737 helix: 2.21 (0.21), residues: 679 sheet: 0.28 (0.17), residues: 900 loop : -0.91 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 104 HIS 0.004 0.001 HIS C 519 PHE 0.022 0.001 PHE A 374 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8744 (m-80) cc_final: 0.8317 (m-80) REVERT: A 1050 MET cc_start: 0.8833 (ptt) cc_final: 0.8623 (ptt) REVERT: B 582 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8922 (tp) REVERT: B 1005 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8076 (tm-30) REVERT: C 115 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7502 (tp40) REVERT: C 985 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8551 (m-30) REVERT: D 4 MET cc_start: 0.6793 (ptp) cc_final: 0.6357 (ptp) REVERT: H 24 GLN cc_start: 0.8733 (tt0) cc_final: 0.8361 (tm-30) REVERT: I 34 MET cc_start: 0.2827 (tmm) cc_final: 0.2532 (ppp) outliers start: 31 outliers final: 23 residues processed: 116 average time/residue: 0.4018 time to fit residues: 79.5883 Evaluate side-chains 109 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 267 optimal weight: 10.0000 chunk 206 optimal weight: 30.0000 chunk 307 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 364 optimal weight: 40.0000 chunk 228 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30840 Z= 0.344 Angle : 0.556 9.490 41966 Z= 0.286 Chirality : 0.043 0.282 4878 Planarity : 0.004 0.043 5347 Dihedral : 5.522 59.750 4990 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.03 % Favored : 94.92 % Rotamer: Outliers : 1.25 % Allowed : 11.31 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3737 helix: 1.98 (0.21), residues: 685 sheet: 0.18 (0.17), residues: 948 loop : -0.97 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 258 HIS 0.009 0.001 HIS B 519 PHE 0.022 0.001 PHE A 374 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 87 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8767 (m-80) cc_final: 0.8335 (m-80) REVERT: A 1050 MET cc_start: 0.8844 (ptt) cc_final: 0.8580 (ptt) REVERT: B 1005 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8154 (tm-30) REVERT: C 115 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7634 (tp40) REVERT: D 4 MET cc_start: 0.6786 (ptp) cc_final: 0.6146 (ptp) REVERT: E 32 TYR cc_start: 0.8444 (m-80) cc_final: 0.8211 (m-80) REVERT: E 61 TYR cc_start: 0.9266 (m-10) cc_final: 0.8979 (m-10) REVERT: H 24 GLN cc_start: 0.8729 (tt0) cc_final: 0.8353 (tm-30) REVERT: I 34 MET cc_start: 0.2560 (tmm) cc_final: 0.2259 (ppp) outliers start: 41 outliers final: 35 residues processed: 121 average time/residue: 0.4060 time to fit residues: 84.9815 Evaluate side-chains 119 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 83 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.3980 chunk 145 optimal weight: 30.0000 chunk 217 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30840 Z= 0.149 Angle : 0.493 11.021 41966 Z= 0.254 Chirality : 0.043 0.341 4878 Planarity : 0.004 0.047 5347 Dihedral : 5.191 59.950 4990 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 1.01 % Allowed : 12.02 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3737 helix: 2.28 (0.21), residues: 679 sheet: 0.30 (0.17), residues: 923 loop : -0.92 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.005 0.001 HIS B 519 PHE 0.027 0.001 PHE A 374 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8734 (m-80) cc_final: 0.8309 (m-80) REVERT: B 1005 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 115 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7233 (tp40) REVERT: C 959 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9292 (mp) REVERT: D 4 MET cc_start: 0.6855 (ptp) cc_final: 0.6250 (ptp) REVERT: E 32 TYR cc_start: 0.8399 (m-80) cc_final: 0.8178 (m-80) REVERT: E 61 TYR cc_start: 0.9259 (m-10) cc_final: 0.8990 (m-10) REVERT: H 24 GLN cc_start: 0.8728 (tt0) cc_final: 0.8356 (tm-30) REVERT: I 34 MET cc_start: 0.2928 (tmm) cc_final: 0.2639 (ppp) outliers start: 33 outliers final: 28 residues processed: 119 average time/residue: 0.4046 time to fit residues: 82.3422 Evaluate side-chains 116 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 2.9990 chunk 349 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 339 optimal weight: 6.9990 chunk 348 optimal weight: 0.5980 chunk 204 optimal weight: 0.5980 chunk 147 optimal weight: 20.0000 chunk 266 optimal weight: 5.9990 chunk 104 optimal weight: 0.0870 chunk 306 optimal weight: 3.9990 chunk 321 optimal weight: 30.0000 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30840 Z= 0.209 Angle : 0.505 14.249 41966 Z= 0.259 Chirality : 0.043 0.294 4878 Planarity : 0.004 0.048 5347 Dihedral : 5.112 59.568 4990 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.75 % Rotamer: Outliers : 1.10 % Allowed : 12.17 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3737 helix: 2.27 (0.21), residues: 680 sheet: 0.27 (0.17), residues: 930 loop : -0.91 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 112 HIS 0.004 0.001 HIS C 519 PHE 0.031 0.001 PHE A 374 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8741 (m-80) cc_final: 0.8319 (m-80) REVERT: B 1005 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8058 (tm-30) REVERT: C 115 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7152 (tp40) REVERT: C 959 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9302 (mp) REVERT: D 4 MET cc_start: 0.6872 (ptp) cc_final: 0.6278 (ptp) REVERT: E 32 TYR cc_start: 0.8426 (m-80) cc_final: 0.8211 (m-80) REVERT: E 61 TYR cc_start: 0.9220 (m-10) cc_final: 0.8978 (m-10) REVERT: H 24 GLN cc_start: 0.8749 (tt0) cc_final: 0.8376 (tm-30) REVERT: I 34 MET cc_start: 0.2901 (tmm) cc_final: 0.2621 (ppp) outliers start: 36 outliers final: 32 residues processed: 117 average time/residue: 0.3836 time to fit residues: 78.3494 Evaluate side-chains 117 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 83 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 40.0000 chunk 222 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 249 optimal weight: 30.0000 chunk 376 optimal weight: 0.0770 chunk 346 optimal weight: 50.0000 chunk 299 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30840 Z= 0.332 Angle : 0.562 14.900 41966 Z= 0.288 Chirality : 0.043 0.297 4878 Planarity : 0.004 0.048 5347 Dihedral : 5.289 55.849 4990 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 1.07 % Allowed : 12.38 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3737 helix: 2.03 (0.21), residues: 691 sheet: 0.12 (0.16), residues: 972 loop : -1.01 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 112 HIS 0.005 0.001 HIS B 519 PHE 0.032 0.001 PHE A 374 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG F 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 81 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8761 (m-80) cc_final: 0.8343 (m-80) REVERT: B 1005 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 115 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6940 (tp40) REVERT: C 959 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9313 (mp) REVERT: D 4 MET cc_start: 0.6813 (ptp) cc_final: 0.6374 (ptp) REVERT: E 32 TYR cc_start: 0.8504 (m-80) cc_final: 0.8292 (m-80) REVERT: E 61 TYR cc_start: 0.9229 (m-10) cc_final: 0.8957 (m-10) REVERT: H 24 GLN cc_start: 0.8748 (tt0) cc_final: 0.8370 (tm-30) REVERT: I 34 MET cc_start: 0.2416 (tmm) cc_final: 0.2059 (ppp) REVERT: I 83 MET cc_start: 0.3273 (pmm) cc_final: 0.3062 (pmm) outliers start: 35 outliers final: 32 residues processed: 112 average time/residue: 0.3780 time to fit residues: 75.5991 Evaluate side-chains 115 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 319 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 276 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 308 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.086104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054019 restraints weight = 139550.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.055597 restraints weight = 68266.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.055388 restraints weight = 39198.459| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 30840 Z= 0.144 Angle : 0.498 15.114 41966 Z= 0.257 Chirality : 0.042 0.267 4878 Planarity : 0.004 0.048 5347 Dihedral : 4.975 55.088 4990 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 0.82 % Allowed : 12.69 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3737 helix: 2.22 (0.21), residues: 691 sheet: 0.26 (0.16), residues: 933 loop : -0.96 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 112 HIS 0.004 0.001 HIS C 519 PHE 0.035 0.001 PHE A 374 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG F 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4494.50 seconds wall clock time: 84 minutes 38.70 seconds (5078.70 seconds total)