Starting phenix.real_space_refine on Mon Mar 25 19:50:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/03_2024/7r4r_14315_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/03_2024/7r4r_14315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/03_2024/7r4r_14315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/03_2024/7r4r_14315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/03_2024/7r4r_14315_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/03_2024/7r4r_14315_trim.pdb" } resolution = 3.9 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= 0.026 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: 5 Type Number sf(0) Gaussians S 119 5.16 5 C 16750 2.51 5 N 4337 2.21 5 O 5128 1.98 5 H 24171 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A VAL 42": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A LEU 922": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B VAL 42": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ARG 646": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B LEU 922": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C VAL 42": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C ARG 646": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C LEU 922": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1146": "OD1" <-> "OD2" 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: 50505 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 16360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 16359 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 16359 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 bond proxies already assigned to first conformer: 16548 Chain: "B" Number of atoms: 16287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 16267 Classifications: {'peptide': 1054} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1000} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1054, 16267 Classifications: {'peptide': 1054} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1000} Chain breaks: 8 bond proxies already assigned to first conformer: 16433 Chain: "C" Number of atoms: 16361 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 bond proxies already assigned to first conformer: 16549 Chain: "D" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 459 " occ=0.60 ... (20 atoms not shown) pdb=" HG BSER B 459 " occ=0.40 Time building chain proxies: 42.59, per 1000 atoms: 0.84 Number of scatterers: 50505 At special positions: 0 Unit cell: (149.6, 159.8, 202.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 O 5128 8.00 N 4337 7.00 C 16750 6.00 H 24171 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.35 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.35 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.35 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1303 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 717 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 61 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG G 1 " - " ASN C 122 " Time building additional restraints: 41.42 Conformation dependent library (CDL) restraints added in 9.5 seconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6158 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 50 sheets defined 23.0% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.983A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 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 885 Processing helix chain 'A' and resid 898 through 910 Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.867A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.994A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.059A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.510A pdb=" N ASN A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A1120 " --> pdb=" O THR A1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1116 through 1120' Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.258A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.751A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.676A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 898 through 910 Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.868A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.993A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.059A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1116 through 1120 removed outlier: 3.509A pdb=" N ASN B1119 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B1120 " --> pdb=" O THR B1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1116 through 1120' Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 4.258A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1146' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.940A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.084A 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 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 898 through 910 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.868A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.993A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.059A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1116 through 1120 removed outlier: 3.510A pdb=" N ASN C1119 " --> pdb=" O THR C1116 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C1120 " --> pdb=" O THR C1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1116 through 1120' Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 4.259A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1146' Processing helix chain 'D' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.939A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.535A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.426A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 316 removed outlier: 6.296A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.503A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 4.328A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 660 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 5.608A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.762A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.821A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.632A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.566A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1121 through 1122 removed outlier: 3.617A pdb=" N HIS A1088 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.939A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.535A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.427A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.512A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 316 removed outlier: 6.295A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.531A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AD1, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AD2, first strand: chain 'B' and resid 659 through 660 Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 5.672A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.762A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.820A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B1060 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 735 removed outlier: 3.631A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1121 through 1122 removed outlier: 3.618A pdb=" N HIS B1088 " --> pdb=" O ILE B1081 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.939A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 49 through 55 Processing sheet with id=AE1, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.536A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.427A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.512A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 309 through 316 removed outlier: 6.295A pdb=" N GLU C 309 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C 601 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.277A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.080A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 659 through 660 Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.762A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.821A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.632A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1121 through 1122 removed outlier: 3.617A pdb=" N HIS C1088 " --> pdb=" O ILE C1081 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 13 removed outlier: 4.379A pdb=" N ARG D 33 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 10 through 13 966 hydrogen bonds defined for protein. 2640 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: 22.34 Time building geometry restraints manager: 42.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.50 - 0.85: 1190 0.85 - 1.21: 23012 1.21 - 1.56: 26520 1.56 - 1.92: 352 1.92 - 2.28: 16 Warning: very small bond lengths. Bond restraints: 51090 Sorted by residual: bond pdb=" CD ARG A 983 " pdb=" HD2 ARG A 983 " ideal model delta sigma weight residual 0.970 1.951 -0.981 2.00e-02 2.50e+03 2.41e+03 bond pdb=" CD ARG B 983 " pdb=" HD2 ARG B 983 " ideal model delta sigma weight residual 0.970 1.942 -0.972 2.00e-02 2.50e+03 2.36e+03 bond pdb=" CD ARG C 983 " pdb=" HD2 ARG C 983 " ideal model delta sigma weight residual 0.970 1.932 -0.962 2.00e-02 2.50e+03 2.31e+03 bond pdb=" CD ARG C 983 " pdb=" HD3 ARG C 983 " ideal model delta sigma weight residual 0.970 1.835 -0.865 2.00e-02 2.50e+03 1.87e+03 bond pdb=" CD ARG B 983 " pdb=" HD3 ARG B 983 " ideal model delta sigma weight residual 0.970 1.822 -0.852 2.00e-02 2.50e+03 1.81e+03 ... (remaining 51085 not shown) Histogram of bond angle deviations from ideal: 17.47 - 49.97: 66 49.97 - 82.47: 1770 82.47 - 114.98: 58937 114.98 - 147.48: 30486 147.48 - 179.98: 84 Bond angle restraints: 91343 Sorted by residual: angle pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " pdb=" NH1 ARG A 983 " ideal model delta sigma weight residual 121.50 57.47 64.03 1.00e+00 1.00e+00 4.10e+03 angle pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " pdb=" NH1 ARG C 983 " ideal model delta sigma weight residual 121.50 57.51 63.99 1.00e+00 1.00e+00 4.09e+03 angle pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " pdb=" NH1 ARG B 983 " ideal model delta sigma weight residual 121.50 57.57 63.93 1.00e+00 1.00e+00 4.09e+03 angle pdb=" CD ARG B 983 " pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " ideal model delta sigma weight residual 124.40 49.50 74.90 1.40e+00 5.10e-01 2.86e+03 angle pdb=" CD ARG C 983 " pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " ideal model delta sigma weight residual 124.40 49.51 74.89 1.40e+00 5.10e-01 2.86e+03 ... (remaining 91338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.91: 23175 31.91 - 63.82: 1842 63.82 - 95.73: 182 95.73 - 127.64: 19 127.64 - 159.55: 6 Dihedral angle restraints: 25224 sinusoidal: 13784 harmonic: 11440 Sorted by residual: dihedral pdb=" CG HIS C1083 " pdb=" ND1 HIS C1083 " pdb=" CE1 HIS C1083 " pdb=" HE1 HIS C1083 " ideal model delta harmonic sigma weight residual -180.00 -20.45 -159.55 0 5.00e+00 4.00e-02 1.02e+03 dihedral pdb=" CG HIS B1083 " pdb=" ND1 HIS B1083 " pdb=" CE1 HIS B1083 " pdb=" HE1 HIS B1083 " ideal model delta harmonic sigma weight residual -180.00 -20.54 -159.46 0 5.00e+00 4.00e-02 1.02e+03 dihedral pdb=" CG HIS A1083 " pdb=" ND1 HIS A1083 " pdb=" CE1 HIS A1083 " pdb=" HE1 HIS A1083 " ideal model delta harmonic sigma weight residual -180.00 -20.68 -159.32 0 5.00e+00 4.00e-02 1.02e+03 ... (remaining 25221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.774: 4147 0.774 - 1.549: 78 1.549 - 2.323: 7 2.323 - 3.098: 12 3.098 - 3.872: 10 Chirality restraints: 4254 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 1.47 -3.87 2.00e-01 2.50e+01 3.75e+02 chirality pdb=" CB ILE A 923 " pdb=" CA ILE A 923 " pdb=" CG1 ILE A 923 " pdb=" CG2 ILE A 923 " both_signs ideal model delta sigma weight residual False 2.64 -0.95 3.59 2.00e-01 2.50e+01 3.23e+02 chirality pdb=" CB ILE C 923 " pdb=" CA ILE C 923 " pdb=" CG1 ILE C 923 " pdb=" CG2 ILE C 923 " both_signs ideal model delta sigma weight residual False 2.64 -0.95 3.59 2.00e-01 2.50e+01 3.23e+02 ... (remaining 4251 not shown) Planarity restraints: 7704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A1083 " 0.098 2.00e-02 2.50e+03 4.10e-01 3.79e+03 pdb=" CG HIS A1083 " 0.182 2.00e-02 2.50e+03 pdb=" ND1 HIS A1083 " 0.557 2.00e-02 2.50e+03 pdb=" CD2 HIS A1083 " -0.597 2.00e-02 2.50e+03 pdb=" CE1 HIS A1083 " 0.431 2.00e-02 2.50e+03 pdb=" NE2 HIS A1083 " -0.592 2.00e-02 2.50e+03 pdb=" HD2 HIS A1083 " -0.324 2.00e-02 2.50e+03 pdb=" HE1 HIS A1083 " 0.382 2.00e-02 2.50e+03 pdb=" HE2 HIS A1083 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B1083 " -0.098 2.00e-02 2.50e+03 4.10e-01 3.79e+03 pdb=" CG HIS B1083 " -0.182 2.00e-02 2.50e+03 pdb=" ND1 HIS B1083 " -0.557 2.00e-02 2.50e+03 pdb=" CD2 HIS B1083 " 0.598 2.00e-02 2.50e+03 pdb=" CE1 HIS B1083 " -0.432 2.00e-02 2.50e+03 pdb=" NE2 HIS B1083 " 0.591 2.00e-02 2.50e+03 pdb=" HD2 HIS B1083 " 0.324 2.00e-02 2.50e+03 pdb=" HE1 HIS B1083 " -0.380 2.00e-02 2.50e+03 pdb=" HE2 HIS B1083 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C1083 " -0.098 2.00e-02 2.50e+03 4.10e-01 3.78e+03 pdb=" CG HIS C1083 " -0.182 2.00e-02 2.50e+03 pdb=" ND1 HIS C1083 " -0.555 2.00e-02 2.50e+03 pdb=" CD2 HIS C1083 " 0.596 2.00e-02 2.50e+03 pdb=" CE1 HIS C1083 " -0.431 2.00e-02 2.50e+03 pdb=" NE2 HIS C1083 " 0.592 2.00e-02 2.50e+03 pdb=" HD2 HIS C1083 " 0.324 2.00e-02 2.50e+03 pdb=" HE1 HIS C1083 " -0.382 2.00e-02 2.50e+03 pdb=" HE2 HIS C1083 " 0.136 2.00e-02 2.50e+03 ... (remaining 7701 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.52: 232 1.52 - 2.29: 16940 2.29 - 3.06: 151266 3.06 - 3.83: 213401 3.83 - 4.60: 334213 Warning: very small nonbonded interaction distances. Nonbonded interactions: 716052 Sorted by model distance: nonbonded pdb=" OE1 GLN B 954 " pdb="HE21 GLN B 954 " model vdw 0.749 1.960 nonbonded pdb=" OE1 GLN C 954 " pdb="HE21 GLN C 954 " model vdw 0.768 1.960 nonbonded pdb=" OE1 GLN A 954 " pdb="HE21 GLN A 954 " model vdw 0.768 1.960 nonbonded pdb=" OE1 GLN C 954 " pdb="HE22 GLN C 954 " model vdw 0.769 1.960 nonbonded pdb=" OE1 GLN A 954 " pdb="HE22 GLN A 954 " model vdw 0.769 1.960 ... (remaining 716047 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 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 577 or (resid 584 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 o \ r name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) o \ r resid 585 through 1063 or (resid 1064 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 1065 through 1146 or resid 1301 through 1307)) selection = (chain 'B' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 656 or (resid 657 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or \ resid 658 through 1146 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 577 or (resid 584 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 o \ r name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) o \ r resid 585 through 656 or (resid 657 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 \ or name HB3)) or resid 658 through 1063 or (resid 1064 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or n \ ame NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or \ name HE2)) or resid 1065 through 1146 or resid 1301 through 1307)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 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: 9.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.740 Extract box with map and model: 28.220 Check model and map are aligned: 0.710 Set scattering table: 0.440 Process input model: 181.620 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 227.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4286 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 : 0.036 0.757 26919 Z= 2.408 Angle : 4.110 74.897 36614 Z= 2.248 Chirality : 0.315 3.872 4254 Planarity : 0.029 0.574 4684 Dihedral : 18.824 113.688 10311 Min Nonbonded Distance : 1.228 Molprobity Statistics. All-atom Clashscore : 59.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.52 % Favored : 91.27 % Rotamer: Outliers : 7.44 % Allowed : 31.12 % Favored : 61.44 % Cbeta Deviations : 4.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.91 % Twisted General : 1.67 % 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: -3.20 (0.13), residues: 3245 helix: -2.02 (0.17), residues: 640 sheet: -1.49 (0.20), residues: 628 loop : -2.48 (0.12), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.124 0.011 TRP C1102 HIS 0.407 0.035 HIS A1083 PHE 0.345 0.013 PHE A 318 TYR 0.178 0.006 TYR A 266 ARG 0.347 0.023 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 510 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.4639 (OUTLIER) cc_final: 0.3616 (t-90) REVERT: A 118 LEU cc_start: 0.8087 (pt) cc_final: 0.7846 (pt) REVERT: A 151 SER cc_start: 0.8040 (t) cc_final: 0.7802 (p) REVERT: A 207 HIS cc_start: 0.5082 (p-80) cc_final: 0.4834 (p-80) REVERT: A 320 VAL cc_start: 0.5457 (OUTLIER) cc_final: 0.5205 (p) REVERT: A 377 PHE cc_start: 0.4313 (OUTLIER) cc_final: 0.3798 (p90) REVERT: A 389 ASP cc_start: 0.5500 (OUTLIER) cc_final: 0.5267 (p0) REVERT: A 398 ASP cc_start: 0.7964 (m-30) cc_final: 0.7738 (p0) REVERT: A 580 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.4819 (mm-40) REVERT: A 767 LEU cc_start: 0.5006 (pp) cc_final: 0.4396 (mp) REVERT: A 858 LEU cc_start: 0.8235 (mt) cc_final: 0.7816 (mm) REVERT: A 933 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7057 (tppp) REVERT: B 133 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.4403 (m-80) REVERT: B 374 PHE cc_start: 0.2682 (OUTLIER) cc_final: -0.2149 (m-80) REVERT: B 393 THR cc_start: 0.5534 (p) cc_final: 0.4747 (p) REVERT: B 440 ASN cc_start: 0.6973 (OUTLIER) cc_final: 0.6761 (p0) REVERT: B 456 PHE cc_start: 0.2835 (OUTLIER) cc_final: 0.1322 (m-80) REVERT: B 516 GLU cc_start: 0.4039 (OUTLIER) cc_final: 0.3162 (mp0) REVERT: B 613 GLN cc_start: 0.5498 (tp40) cc_final: 0.4881 (tp40) REVERT: B 619 GLU cc_start: 0.3124 (OUTLIER) cc_final: 0.2230 (mp0) REVERT: B 931 ILE cc_start: 0.3365 (mm) cc_final: 0.2685 (mm) REVERT: C 47 VAL cc_start: 0.3953 (t) cc_final: 0.3690 (t) REVERT: C 277 LEU cc_start: 0.5657 (mm) cc_final: 0.5166 (mt) REVERT: C 422 ASN cc_start: 0.6323 (OUTLIER) cc_final: 0.5115 (t0) REVERT: C 444 LYS cc_start: 0.3854 (OUTLIER) cc_final: 0.1545 (ttpp) REVERT: C 538 CYS cc_start: 0.1835 (OUTLIER) cc_final: 0.1191 (p) REVERT: C 740 MET cc_start: 0.6755 (ppp) cc_final: 0.6279 (ppp) REVERT: C 900 MET cc_start: 0.1447 (mmm) cc_final: 0.1110 (mmm) REVERT: C 1009 THR cc_start: 0.5703 (p) cc_final: 0.4449 (m) REVERT: C 1038 LYS cc_start: 0.7397 (mmtm) cc_final: 0.7179 (mmtm) REVERT: D 104 CYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5612 (m) outliers start: 211 outliers final: 123 residues processed: 683 average time/residue: 0.9641 time to fit residues: 999.2157 Evaluate side-chains 587 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 448 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 1095 PHE Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1095 PHE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 116 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 297 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 49 HIS B 196 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 563 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN D 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 26919 Z= 0.481 Angle : 1.795 42.788 36614 Z= 0.871 Chirality : 0.223 1.860 4254 Planarity : 0.014 0.349 4684 Dihedral : 15.224 140.615 4755 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 41.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.21 % Favored : 91.55 % Rotamer: Outliers : 11.79 % Allowed : 26.22 % Favored : 62.00 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.67 % 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: -3.13 (0.13), residues: 3245 helix: -1.72 (0.17), residues: 657 sheet: -1.54 (0.19), residues: 671 loop : -2.51 (0.12), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C1102 HIS 0.024 0.003 HIS A1083 PHE 0.086 0.003 PHE C 43 TYR 0.043 0.002 TYR C 279 ARG 0.027 0.002 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 424 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.5277 (OUTLIER) cc_final: 0.4831 (m) REVERT: A 47 VAL cc_start: 0.4984 (OUTLIER) cc_final: 0.4745 (t) REVERT: A 63 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8358 (t) REVERT: A 151 SER cc_start: 0.8002 (t) cc_final: 0.7795 (p) REVERT: A 158 ARG cc_start: 0.6557 (ttp-170) cc_final: 0.6131 (ttm170) REVERT: A 207 HIS cc_start: 0.5584 (p-80) cc_final: 0.5343 (p-80) REVERT: A 212 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5750 (pt) REVERT: A 237 ARG cc_start: 0.6953 (mmm160) cc_final: 0.6697 (mmm-85) REVERT: A 377 PHE cc_start: 0.4495 (OUTLIER) cc_final: 0.4027 (p90) REVERT: A 580 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.4783 (mm-40) REVERT: A 697 MET cc_start: 0.4644 (tpt) cc_final: 0.3796 (tpt) REVERT: A 869 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8040 (ptp) REVERT: B 113 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8960 (tptp) REVERT: B 157 PHE cc_start: 0.3067 (OUTLIER) cc_final: 0.2666 (m-80) REVERT: B 341 VAL cc_start: 0.3778 (OUTLIER) cc_final: 0.2967 (p) REVERT: B 374 PHE cc_start: 0.2637 (OUTLIER) cc_final: -0.2271 (m-80) REVERT: B 440 ASN cc_start: 0.6918 (OUTLIER) cc_final: 0.6715 (p0) REVERT: B 455 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.5568 (mt) REVERT: B 456 PHE cc_start: 0.2969 (OUTLIER) cc_final: 0.1382 (m-80) REVERT: B 490 PHE cc_start: 0.8595 (t80) cc_final: 0.8307 (t80) REVERT: B 611 LEU cc_start: 0.7285 (tt) cc_final: 0.6616 (tp) REVERT: B 613 GLN cc_start: 0.6142 (tp40) cc_final: 0.4799 (tm-30) REVERT: B 710 ASN cc_start: 0.3579 (OUTLIER) cc_final: 0.3267 (p0) REVERT: B 872 GLN cc_start: 0.5673 (OUTLIER) cc_final: 0.5449 (pp30) REVERT: B 888 PHE cc_start: 0.8271 (p90) cc_final: 0.8052 (p90) REVERT: B 894 LEU cc_start: 0.4149 (mt) cc_final: 0.3585 (mm) REVERT: C 54 LEU cc_start: 0.4684 (mt) cc_final: 0.3648 (mt) REVERT: C 153 MET cc_start: 0.5302 (ptp) cc_final: 0.5005 (pmm) REVERT: C 157 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5463 (t80) REVERT: C 160 TYR cc_start: 0.5975 (p90) cc_final: 0.5649 (p90) REVERT: C 422 ASN cc_start: 0.6702 (OUTLIER) cc_final: 0.5469 (t0) REVERT: C 444 LYS cc_start: 0.4062 (OUTLIER) cc_final: 0.1106 (tttt) REVERT: C 448 ASN cc_start: 0.7690 (t0) cc_final: 0.7197 (m-40) REVERT: C 611 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6665 (tp) REVERT: C 646 ARG cc_start: 0.5440 (mmm160) cc_final: 0.5194 (mmp80) REVERT: C 900 MET cc_start: 0.2338 (mmm) cc_final: 0.1732 (mmm) REVERT: C 996 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7357 (tt) REVERT: C 998 THR cc_start: 0.5827 (p) cc_final: 0.4626 (m) REVERT: C 1038 LYS cc_start: 0.7549 (mmtm) cc_final: 0.7324 (mmtm) REVERT: C 1050 MET cc_start: 0.5807 (tpp) cc_final: 0.4978 (tpp) REVERT: C 1145 LEU cc_start: 0.0565 (OUTLIER) cc_final: -0.0791 (tt) REVERT: D 104 CYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5966 (m) outliers start: 336 outliers final: 214 residues processed: 687 average time/residue: 0.8657 time to fit residues: 930.1128 Evaluate side-chains 646 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 409 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 104 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 0.0970 chunk 202 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 chunk 322 optimal weight: 10.0000 chunk 265 optimal weight: 0.6980 chunk 295 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 239 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 925 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 388 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4629 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 26919 Z= 0.344 Angle : 1.485 34.609 36614 Z= 0.738 Chirality : 0.234 1.792 4254 Planarity : 0.008 0.201 4684 Dihedral : 13.086 173.222 4645 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 32.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.86 % Favored : 90.99 % Rotamer: Outliers : 9.53 % Allowed : 27.33 % Favored : 63.14 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -2.85 (0.13), residues: 3245 helix: -1.14 (0.18), residues: 652 sheet: -1.51 (0.19), residues: 681 loop : -2.40 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C1102 HIS 0.010 0.002 HIS B 245 PHE 0.044 0.002 PHE C 43 TYR 0.025 0.002 TYR B 37 ARG 0.011 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 421 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.5856 (p-80) cc_final: 0.5565 (p-80) REVERT: A 237 ARG cc_start: 0.6946 (mmm160) cc_final: 0.6727 (mmm-85) REVERT: A 316 SER cc_start: -0.0577 (OUTLIER) cc_final: -0.1268 (t) REVERT: A 377 PHE cc_start: 0.4647 (OUTLIER) cc_final: 0.4139 (p90) REVERT: A 580 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.4915 (mm-40) REVERT: A 697 MET cc_start: 0.4832 (tpt) cc_final: 0.4632 (tpt) REVERT: A 703 ASN cc_start: 0.6177 (OUTLIER) cc_final: 0.5661 (t0) REVERT: A 731 MET cc_start: 0.5430 (ttm) cc_final: 0.5135 (ttm) REVERT: A 925 ASN cc_start: 0.8945 (m-40) cc_final: 0.8737 (m-40) REVERT: A 947 LYS cc_start: 0.8149 (tppt) cc_final: 0.7865 (tppt) REVERT: A 1094 VAL cc_start: 0.4127 (m) cc_final: 0.3534 (t) REVERT: B 106 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5193 (m-80) REVERT: B 220 PHE cc_start: 0.4906 (OUTLIER) cc_final: 0.4071 (t80) REVERT: B 374 PHE cc_start: 0.2586 (OUTLIER) cc_final: -0.2291 (m-80) REVERT: B 440 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6688 (p0) REVERT: B 451 TYR cc_start: 0.7574 (m-10) cc_final: 0.7188 (m-10) REVERT: B 455 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5211 (mt) REVERT: B 456 PHE cc_start: 0.2825 (OUTLIER) cc_final: 0.1282 (m-80) REVERT: B 490 PHE cc_start: 0.8579 (t80) cc_final: 0.8298 (t80) REVERT: B 539 VAL cc_start: 0.5274 (OUTLIER) cc_final: 0.5058 (m) REVERT: B 613 GLN cc_start: 0.6207 (tp40) cc_final: 0.5199 (tm-30) REVERT: B 655 HIS cc_start: 0.7015 (t-90) cc_final: 0.6657 (m170) REVERT: B 888 PHE cc_start: 0.8282 (p90) cc_final: 0.8009 (p90) REVERT: C 54 LEU cc_start: 0.4368 (mt) cc_final: 0.3297 (mt) REVERT: C 153 MET cc_start: 0.5005 (ptp) cc_final: 0.4624 (pmm) REVERT: C 160 TYR cc_start: 0.6089 (p90) cc_final: 0.5644 (p90) REVERT: C 177 MET cc_start: 0.1476 (mtm) cc_final: 0.1166 (mtm) REVERT: C 422 ASN cc_start: 0.6833 (OUTLIER) cc_final: 0.5523 (t0) REVERT: C 444 LYS cc_start: 0.3861 (OUTLIER) cc_final: 0.1397 (tttm) REVERT: C 448 ASN cc_start: 0.7662 (t0) cc_final: 0.7126 (m-40) REVERT: C 529 LYS cc_start: 0.3309 (OUTLIER) cc_final: -0.1568 (pttt) REVERT: C 646 ARG cc_start: 0.5592 (mmm160) cc_final: 0.5374 (mmp80) REVERT: C 900 MET cc_start: 0.2097 (mmm) cc_final: 0.1457 (mmm) REVERT: C 996 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7362 (tt) REVERT: C 1038 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7413 (mmtm) REVERT: C 1145 LEU cc_start: 0.0890 (OUTLIER) cc_final: 0.0178 (tt) outliers start: 271 outliers final: 198 residues processed: 634 average time/residue: 0.9032 time to fit residues: 886.0523 Evaluate side-chains 621 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 407 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 317 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 283 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1010 GLN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4892 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 26919 Z= 0.329 Angle : 1.413 37.934 36614 Z= 0.709 Chirality : 0.238 1.807 4254 Planarity : 0.006 0.076 4684 Dihedral : 11.721 179.551 4623 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 32.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.33 % Rotamer: Outliers : 8.45 % Allowed : 28.16 % Favored : 63.39 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.74 (0.13), residues: 3245 helix: -0.99 (0.19), residues: 656 sheet: -1.51 (0.19), residues: 668 loop : -2.32 (0.12), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 353 HIS 0.011 0.002 HIS A 245 PHE 0.033 0.002 PHE A 106 TYR 0.021 0.002 TYR C 279 ARG 0.010 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 425 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7105 (pp) cc_final: 0.6890 (pt) REVERT: A 158 ARG cc_start: 0.7214 (ttm170) cc_final: 0.6933 (ttm170) REVERT: A 220 PHE cc_start: 0.5609 (OUTLIER) cc_final: 0.5168 (t80) REVERT: A 238 PHE cc_start: 0.7904 (p90) cc_final: 0.7585 (p90) REVERT: A 368 LEU cc_start: 0.2549 (OUTLIER) cc_final: 0.1347 (tp) REVERT: A 377 PHE cc_start: 0.4577 (OUTLIER) cc_final: 0.4105 (p90) REVERT: A 580 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.5234 (mm110) REVERT: A 947 LYS cc_start: 0.8173 (tppt) cc_final: 0.7671 (tppt) REVERT: A 952 VAL cc_start: 0.7357 (m) cc_final: 0.6999 (t) REVERT: A 1094 VAL cc_start: 0.4745 (m) cc_final: 0.4222 (t) REVERT: B 220 PHE cc_start: 0.5254 (OUTLIER) cc_final: 0.5047 (t80) REVERT: B 266 TYR cc_start: 0.6704 (m-80) cc_final: 0.6330 (m-80) REVERT: B 374 PHE cc_start: 0.2748 (OUTLIER) cc_final: -0.2182 (m-80) REVERT: B 451 TYR cc_start: 0.7711 (m-10) cc_final: 0.7309 (m-10) REVERT: B 455 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5241 (mt) REVERT: B 456 PHE cc_start: 0.3046 (OUTLIER) cc_final: 0.1507 (m-80) REVERT: B 490 PHE cc_start: 0.8632 (t80) cc_final: 0.8356 (t80) REVERT: B 539 VAL cc_start: 0.5190 (OUTLIER) cc_final: 0.4985 (m) REVERT: B 560 LEU cc_start: 0.0091 (OUTLIER) cc_final: -0.0689 (mt) REVERT: B 563 GLN cc_start: 0.2569 (OUTLIER) cc_final: 0.2141 (mt0) REVERT: B 613 GLN cc_start: 0.6416 (tp40) cc_final: 0.5507 (tm-30) REVERT: B 655 HIS cc_start: 0.7191 (t-90) cc_final: 0.6854 (m-70) REVERT: B 735 SER cc_start: 0.6825 (OUTLIER) cc_final: 0.6455 (p) REVERT: B 872 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5732 (pp30) REVERT: C 138 ASP cc_start: 0.7809 (p0) cc_final: 0.7595 (t0) REVERT: C 160 TYR cc_start: 0.6209 (p90) cc_final: 0.5756 (p90) REVERT: C 177 MET cc_start: 0.1641 (mtm) cc_final: 0.1293 (mtm) REVERT: C 444 LYS cc_start: 0.4100 (OUTLIER) cc_final: 0.1716 (tttm) REVERT: C 448 ASN cc_start: 0.7772 (t0) cc_final: 0.7187 (m-40) REVERT: C 529 LYS cc_start: 0.3903 (OUTLIER) cc_final: 0.1818 (pptt) REVERT: C 646 ARG cc_start: 0.6113 (mmm160) cc_final: 0.5886 (mmp80) REVERT: C 740 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6043 (ppp) REVERT: C 822 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6652 (mm) REVERT: C 900 MET cc_start: 0.2507 (mmm) cc_final: 0.1811 (mmm) REVERT: C 1007 TYR cc_start: 0.7101 (t80) cc_final: 0.6425 (t80) REVERT: C 1038 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7668 (mmtm) REVERT: C 1113 GLN cc_start: 0.2709 (OUTLIER) cc_final: 0.2352 (pm20) outliers start: 240 outliers final: 190 residues processed: 608 average time/residue: 0.9125 time to fit residues: 854.1639 Evaluate side-chains 621 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 413 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1023 ASN Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 314 GLN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1101 HIS B 81 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 26919 Z= 0.309 Angle : 1.371 33.850 36614 Z= 0.692 Chirality : 0.238 1.778 4254 Planarity : 0.005 0.061 4684 Dihedral : 11.032 177.687 4600 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 30.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.73 % Favored : 91.14 % Rotamer: Outliers : 8.34 % Allowed : 28.48 % Favored : 63.18 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.13), residues: 3245 helix: -0.65 (0.19), residues: 647 sheet: -1.43 (0.19), residues: 669 loop : -2.25 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 353 HIS 0.009 0.002 HIS A 66 PHE 0.028 0.002 PHE A 318 TYR 0.017 0.002 TYR A 160 ARG 0.008 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 423 time to evaluate : 3.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8542 (t80) cc_final: 0.8278 (m-80) REVERT: A 159 VAL cc_start: 0.5782 (OUTLIER) cc_final: 0.4373 (t) REVERT: A 160 TYR cc_start: 0.8122 (p90) cc_final: 0.7796 (p90) REVERT: A 207 HIS cc_start: 0.6228 (p-80) cc_final: 0.5686 (p-80) REVERT: A 220 PHE cc_start: 0.5826 (OUTLIER) cc_final: 0.5622 (t80) REVERT: A 368 LEU cc_start: 0.2387 (OUTLIER) cc_final: 0.1199 (tp) REVERT: A 377 PHE cc_start: 0.4791 (OUTLIER) cc_final: 0.4217 (p90) REVERT: A 580 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.5498 (mm110) REVERT: A 864 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 952 VAL cc_start: 0.7784 (m) cc_final: 0.7390 (t) REVERT: B 220 PHE cc_start: 0.5660 (OUTLIER) cc_final: 0.4961 (t80) REVERT: B 374 PHE cc_start: 0.2903 (OUTLIER) cc_final: -0.2168 (m-80) REVERT: B 451 TYR cc_start: 0.7832 (m-10) cc_final: 0.7386 (m-10) REVERT: B 455 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5342 (mt) REVERT: B 456 PHE cc_start: 0.3343 (OUTLIER) cc_final: 0.1821 (m-80) REVERT: B 490 PHE cc_start: 0.8634 (t80) cc_final: 0.8339 (t80) REVERT: B 560 LEU cc_start: 0.0388 (OUTLIER) cc_final: -0.0301 (mt) REVERT: B 563 GLN cc_start: 0.3010 (OUTLIER) cc_final: 0.2687 (mt0) REVERT: B 613 GLN cc_start: 0.6566 (tp40) cc_final: 0.5769 (tm-30) REVERT: B 735 SER cc_start: 0.6747 (OUTLIER) cc_final: 0.6180 (p) REVERT: B 743 CYS cc_start: 0.3539 (OUTLIER) cc_final: 0.3158 (p) REVERT: B 868 GLU cc_start: 0.3921 (OUTLIER) cc_final: 0.3470 (mm-30) REVERT: B 872 GLN cc_start: 0.6048 (OUTLIER) cc_final: 0.5805 (pp30) REVERT: B 913 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7013 (mm-40) REVERT: C 160 TYR cc_start: 0.6321 (p90) cc_final: 0.5829 (p90) REVERT: C 177 MET cc_start: 0.1715 (mtm) cc_final: 0.1382 (mtm) REVERT: C 231 ILE cc_start: 0.4066 (OUTLIER) cc_final: 0.2919 (pt) REVERT: C 444 LYS cc_start: 0.3874 (OUTLIER) cc_final: 0.0989 (tttm) REVERT: C 448 ASN cc_start: 0.7783 (t0) cc_final: 0.7138 (m-40) REVERT: C 529 LYS cc_start: 0.4505 (OUTLIER) cc_final: -0.0190 (pttt) REVERT: C 646 ARG cc_start: 0.6428 (mmm160) cc_final: 0.6192 (mmp80) REVERT: C 740 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6232 (ppp) REVERT: C 818 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5392 (mp) REVERT: C 900 MET cc_start: 0.2614 (mmm) cc_final: 0.1919 (mmm) REVERT: C 988 GLU cc_start: 0.8540 (mp0) cc_final: 0.8326 (mp0) REVERT: C 1007 TYR cc_start: 0.7130 (t80) cc_final: 0.6500 (t80) REVERT: C 1038 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7821 (mmtm) REVERT: C 1103 PHE cc_start: 0.5678 (p90) cc_final: 0.5086 (p90) REVERT: C 1113 GLN cc_start: 0.2937 (OUTLIER) cc_final: 0.2641 (pm20) outliers start: 237 outliers final: 185 residues processed: 593 average time/residue: 0.9065 time to fit residues: 821.7699 Evaluate side-chains 618 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 410 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 6.9990 chunk 285 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 317 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5206 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26919 Z= 0.313 Angle : 1.374 36.226 36614 Z= 0.693 Chirality : 0.240 1.814 4254 Planarity : 0.005 0.067 4684 Dihedral : 10.757 178.563 4591 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 33.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.32 % Favored : 90.59 % Rotamer: Outliers : 8.34 % Allowed : 28.55 % Favored : 63.11 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.13), residues: 3245 helix: -0.71 (0.19), residues: 650 sheet: -1.48 (0.19), residues: 673 loop : -2.26 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 64 HIS 0.023 0.002 HIS C1101 PHE 0.022 0.002 PHE A 43 TYR 0.018 0.002 TYR A 160 ARG 0.007 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 421 time to evaluate : 3.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6882 (t80) cc_final: 0.6520 (t80) REVERT: A 129 LYS cc_start: 0.8729 (mttt) cc_final: 0.8338 (mmtt) REVERT: A 144 TYR cc_start: 0.8552 (t80) cc_final: 0.8247 (m-80) REVERT: A 159 VAL cc_start: 0.6082 (OUTLIER) cc_final: 0.4693 (t) REVERT: A 160 TYR cc_start: 0.8158 (p90) cc_final: 0.7811 (p90) REVERT: A 207 HIS cc_start: 0.6385 (p-80) cc_final: 0.6131 (p-80) REVERT: A 368 LEU cc_start: 0.2470 (OUTLIER) cc_final: 0.1330 (tp) REVERT: A 377 PHE cc_start: 0.4907 (OUTLIER) cc_final: 0.4430 (p90) REVERT: A 947 LYS cc_start: 0.8390 (tppt) cc_final: 0.7852 (tppt) REVERT: A 952 VAL cc_start: 0.8018 (m) cc_final: 0.7622 (t) REVERT: A 1051 SER cc_start: 0.8444 (m) cc_final: 0.8145 (p) REVERT: B 64 TRP cc_start: 0.6029 (t-100) cc_final: 0.5668 (t-100) REVERT: B 374 PHE cc_start: 0.2840 (OUTLIER) cc_final: -0.2175 (m-80) REVERT: B 455 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.5556 (mt) REVERT: B 456 PHE cc_start: 0.3580 (OUTLIER) cc_final: 0.2082 (m-80) REVERT: B 490 PHE cc_start: 0.8613 (t80) cc_final: 0.8332 (t80) REVERT: B 560 LEU cc_start: 0.0699 (OUTLIER) cc_final: -0.0156 (mt) REVERT: B 563 GLN cc_start: 0.3297 (OUTLIER) cc_final: 0.2913 (mt0) REVERT: B 613 GLN cc_start: 0.6710 (tp40) cc_final: 0.5925 (tm-30) REVERT: B 735 SER cc_start: 0.7032 (OUTLIER) cc_final: 0.6296 (p) REVERT: B 749 CYS cc_start: 0.7363 (m) cc_final: 0.6944 (m) REVERT: B 868 GLU cc_start: 0.4123 (OUTLIER) cc_final: 0.3541 (mm-30) REVERT: B 872 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.5850 (pp30) REVERT: B 913 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7230 (mm-40) REVERT: B 933 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6349 (ttpp) REVERT: B 1091 ARG cc_start: 0.2156 (OUTLIER) cc_final: 0.0690 (ptp-170) REVERT: C 160 TYR cc_start: 0.6446 (p90) cc_final: 0.5911 (p90) REVERT: C 177 MET cc_start: 0.1745 (mtm) cc_final: 0.1470 (mtm) REVERT: C 444 LYS cc_start: 0.3856 (OUTLIER) cc_final: 0.1694 (tttm) REVERT: C 646 ARG cc_start: 0.6606 (mmm160) cc_final: 0.6368 (mmp80) REVERT: C 740 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6291 (ppp) REVERT: C 822 LEU cc_start: 0.7210 (mt) cc_final: 0.6881 (mt) REVERT: C 900 MET cc_start: 0.2785 (mmm) cc_final: 0.2082 (mmm) REVERT: C 1007 TYR cc_start: 0.7242 (t80) cc_final: 0.6587 (t80) REVERT: C 1038 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7928 (mmtm) REVERT: C 1103 PHE cc_start: 0.5754 (p90) cc_final: 0.5165 (p90) REVERT: C 1145 LEU cc_start: 0.2437 (OUTLIER) cc_final: 0.2094 (tt) outliers start: 237 outliers final: 197 residues processed: 594 average time/residue: 0.8828 time to fit residues: 794.7657 Evaluate side-chains 623 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 409 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 316 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 26919 Z= 0.315 Angle : 1.360 39.650 36614 Z= 0.690 Chirality : 0.240 1.863 4254 Planarity : 0.005 0.071 4684 Dihedral : 10.397 179.997 4581 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 33.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.69 % Favored : 90.19 % Rotamer: Outliers : 7.89 % Allowed : 28.69 % Favored : 63.42 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.13 % 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: -2.63 (0.13), residues: 3245 helix: -0.76 (0.19), residues: 656 sheet: -1.48 (0.20), residues: 640 loop : -2.28 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 64 HIS 0.009 0.002 HIS A1088 PHE 0.021 0.002 PHE B 43 TYR 0.022 0.002 TYR A 160 ARG 0.007 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 448 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6273 (m-80) cc_final: 0.5994 (m-80) REVERT: A 92 PHE cc_start: 0.7036 (t80) cc_final: 0.6666 (t80) REVERT: A 129 LYS cc_start: 0.8763 (mttt) cc_final: 0.8323 (mmtt) REVERT: A 159 VAL cc_start: 0.6345 (OUTLIER) cc_final: 0.4800 (t) REVERT: A 160 TYR cc_start: 0.8135 (p90) cc_final: 0.7787 (p90) REVERT: A 207 HIS cc_start: 0.6402 (p-80) cc_final: 0.6109 (p-80) REVERT: A 368 LEU cc_start: 0.2586 (OUTLIER) cc_final: 0.1465 (tp) REVERT: A 377 PHE cc_start: 0.4869 (OUTLIER) cc_final: 0.4455 (p90) REVERT: A 947 LYS cc_start: 0.8434 (tppt) cc_final: 0.7916 (tppt) REVERT: A 952 VAL cc_start: 0.8395 (m) cc_final: 0.8012 (t) REVERT: A 1051 SER cc_start: 0.8560 (m) cc_final: 0.8295 (p) REVERT: A 1103 PHE cc_start: 0.5126 (m-80) cc_final: 0.3566 (m-10) REVERT: B 64 TRP cc_start: 0.6196 (t-100) cc_final: 0.5771 (t-100) REVERT: B 374 PHE cc_start: 0.2778 (OUTLIER) cc_final: -0.1344 (m-80) REVERT: B 455 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.5575 (mt) REVERT: B 456 PHE cc_start: 0.3555 (OUTLIER) cc_final: 0.2011 (m-80) REVERT: B 490 PHE cc_start: 0.8590 (t80) cc_final: 0.8384 (t80) REVERT: B 560 LEU cc_start: 0.1046 (OUTLIER) cc_final: 0.0494 (mp) REVERT: B 563 GLN cc_start: 0.3526 (OUTLIER) cc_final: 0.3088 (mt0) REVERT: B 613 GLN cc_start: 0.6812 (tp40) cc_final: 0.6066 (tm-30) REVERT: B 735 SER cc_start: 0.7122 (OUTLIER) cc_final: 0.6404 (p) REVERT: B 872 GLN cc_start: 0.6240 (OUTLIER) cc_final: 0.6000 (pp30) REVERT: B 913 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7416 (mm-40) REVERT: B 933 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6508 (ttpp) REVERT: B 983 ARG cc_start: 0.8027 (tmm-80) cc_final: 0.7562 (tmm-80) REVERT: C 158 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.5480 (tmm-80) REVERT: C 160 TYR cc_start: 0.6540 (p90) cc_final: 0.5982 (p90) REVERT: C 177 MET cc_start: 0.1833 (mtm) cc_final: 0.1518 (mtm) REVERT: C 444 LYS cc_start: 0.3796 (OUTLIER) cc_final: 0.1392 (tttm) REVERT: C 448 ASN cc_start: 0.7906 (t0) cc_final: 0.7321 (m-40) REVERT: C 595 VAL cc_start: 0.7812 (t) cc_final: 0.7255 (t) REVERT: C 646 ARG cc_start: 0.6867 (mmm160) cc_final: 0.6605 (mmp80) REVERT: C 740 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6488 (ppp) REVERT: C 822 LEU cc_start: 0.7380 (mt) cc_final: 0.6974 (mt) REVERT: C 900 MET cc_start: 0.2857 (mmm) cc_final: 0.2153 (mmm) REVERT: C 1007 TYR cc_start: 0.7367 (t80) cc_final: 0.6726 (t80) REVERT: C 1038 LYS cc_start: 0.8290 (mmtm) cc_final: 0.8017 (mmtm) REVERT: C 1145 LEU cc_start: 0.2712 (OUTLIER) cc_final: 0.2374 (tt) outliers start: 224 outliers final: 192 residues processed: 607 average time/residue: 0.9154 time to fit residues: 845.5397 Evaluate side-chains 641 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 433 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 0.0670 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 61 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 536 ASN A 563 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 331 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5244 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26919 Z= 0.267 Angle : 1.327 32.274 36614 Z= 0.672 Chirality : 0.240 1.838 4254 Planarity : 0.005 0.068 4684 Dihedral : 9.943 178.850 4570 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.27 % Favored : 91.61 % Rotamer: Outliers : 6.36 % Allowed : 30.39 % Favored : 63.25 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.14), residues: 3245 helix: -0.39 (0.19), residues: 658 sheet: -1.41 (0.20), residues: 659 loop : -2.12 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 64 HIS 0.009 0.001 HIS A1088 PHE 0.022 0.001 PHE A 43 TYR 0.014 0.001 TYR A 495 ARG 0.007 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 435 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7054 (t80) cc_final: 0.6651 (t80) REVERT: A 129 LYS cc_start: 0.8739 (mttt) cc_final: 0.8313 (mmtt) REVERT: A 159 VAL cc_start: 0.6249 (OUTLIER) cc_final: 0.4919 (t) REVERT: A 160 TYR cc_start: 0.8047 (p90) cc_final: 0.7743 (p90) REVERT: A 207 HIS cc_start: 0.6466 (p-80) cc_final: 0.6186 (p-80) REVERT: A 237 ARG cc_start: 0.7051 (tpt170) cc_final: 0.6642 (tpt170) REVERT: A 300 LYS cc_start: 0.8488 (mttt) cc_final: 0.8278 (mtmm) REVERT: A 368 LEU cc_start: 0.2393 (OUTLIER) cc_final: 0.1291 (tp) REVERT: A 947 LYS cc_start: 0.8401 (tppt) cc_final: 0.7865 (tppt) REVERT: A 952 VAL cc_start: 0.8470 (m) cc_final: 0.8081 (t) REVERT: A 1103 PHE cc_start: 0.4658 (m-80) cc_final: 0.2807 (m-10) REVERT: B 64 TRP cc_start: 0.6133 (t-100) cc_final: 0.5732 (t-100) REVERT: B 374 PHE cc_start: 0.2675 (OUTLIER) cc_final: -0.1424 (m-80) REVERT: B 455 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5287 (mt) REVERT: B 456 PHE cc_start: 0.3517 (OUTLIER) cc_final: 0.1975 (m-80) REVERT: B 560 LEU cc_start: 0.0869 (OUTLIER) cc_final: 0.0494 (mt) REVERT: B 563 GLN cc_start: 0.3253 (OUTLIER) cc_final: 0.2904 (mt0) REVERT: B 613 GLN cc_start: 0.6659 (tp40) cc_final: 0.6115 (tm-30) REVERT: B 735 SER cc_start: 0.6964 (OUTLIER) cc_final: 0.6328 (p) REVERT: B 776 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8489 (ptpp) REVERT: B 787 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7654 (tp-100) REVERT: B 983 ARG cc_start: 0.8012 (tmm-80) cc_final: 0.7539 (tmm-80) REVERT: C 158 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.5062 (tmm-80) REVERT: C 160 TYR cc_start: 0.6384 (p90) cc_final: 0.5848 (p90) REVERT: C 177 MET cc_start: 0.1719 (mtm) cc_final: 0.1422 (mtm) REVERT: C 444 LYS cc_start: 0.3452 (OUTLIER) cc_final: 0.0825 (tttm) REVERT: C 448 ASN cc_start: 0.7801 (t0) cc_final: 0.7154 (m-40) REVERT: C 529 LYS cc_start: 0.5437 (OUTLIER) cc_final: 0.1143 (pttt) REVERT: C 646 ARG cc_start: 0.6908 (mmm160) cc_final: 0.6658 (mmp80) REVERT: C 740 MET cc_start: 0.6904 (ppp) cc_final: 0.6329 (ppp) REVERT: C 778 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.7121 (p) REVERT: C 900 MET cc_start: 0.2488 (mmm) cc_final: 0.1759 (mmm) REVERT: C 964 LYS cc_start: 0.8122 (tptp) cc_final: 0.7736 (tppp) REVERT: C 1007 TYR cc_start: 0.7199 (t80) cc_final: 0.6531 (t80) REVERT: C 1038 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7981 (mmtm) REVERT: C 1145 LEU cc_start: 0.2809 (OUTLIER) cc_final: 0.2479 (tt) outliers start: 180 outliers final: 155 residues processed: 573 average time/residue: 0.9165 time to fit residues: 798.1135 Evaluate side-chains 591 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 423 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.6998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 26919 Z= 0.331 Angle : 1.339 32.753 36614 Z= 0.683 Chirality : 0.240 1.818 4254 Planarity : 0.005 0.071 4684 Dihedral : 9.897 179.544 4560 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 33.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.66 % Favored : 90.25 % Rotamer: Outliers : 6.61 % Allowed : 29.73 % Favored : 63.66 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.06 % 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: -2.51 (0.14), residues: 3245 helix: -0.61 (0.19), residues: 653 sheet: -1.37 (0.20), residues: 637 loop : -2.23 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.008 0.002 HIS A1088 PHE 0.021 0.002 PHE A 43 TYR 0.024 0.002 TYR C 37 ARG 0.007 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 437 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7240 (t80) cc_final: 0.6820 (t80) REVERT: A 129 LYS cc_start: 0.8783 (mttt) cc_final: 0.8366 (mmtt) REVERT: A 207 HIS cc_start: 0.6509 (p-80) cc_final: 0.6208 (p-80) REVERT: A 301 CYS cc_start: 0.7721 (p) cc_final: 0.7480 (p) REVERT: A 368 LEU cc_start: 0.2475 (OUTLIER) cc_final: 0.1376 (tp) REVERT: A 377 PHE cc_start: 0.4841 (OUTLIER) cc_final: 0.4479 (p90) REVERT: A 952 VAL cc_start: 0.8608 (m) cc_final: 0.8229 (t) REVERT: A 1094 VAL cc_start: 0.6041 (OUTLIER) cc_final: 0.5537 (t) REVERT: A 1103 PHE cc_start: 0.5130 (m-80) cc_final: 0.3608 (m-80) REVERT: B 64 TRP cc_start: 0.6335 (t-100) cc_final: 0.5906 (t-100) REVERT: B 374 PHE cc_start: 0.2817 (OUTLIER) cc_final: -0.1290 (m-80) REVERT: B 455 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.5196 (mp) REVERT: B 456 PHE cc_start: 0.3612 (OUTLIER) cc_final: 0.2060 (m-80) REVERT: B 613 GLN cc_start: 0.6873 (tp40) cc_final: 0.6143 (tm-30) REVERT: B 735 SER cc_start: 0.7252 (OUTLIER) cc_final: 0.6518 (p) REVERT: B 902 MET cc_start: 0.7057 (ttp) cc_final: 0.6498 (ttp) REVERT: B 983 ARG cc_start: 0.8085 (tmm-80) cc_final: 0.7605 (tmm-80) REVERT: C 160 TYR cc_start: 0.6491 (p90) cc_final: 0.5941 (p90) REVERT: C 177 MET cc_start: 0.1717 (mtm) cc_final: 0.1403 (mtm) REVERT: C 444 LYS cc_start: 0.3729 (OUTLIER) cc_final: 0.1039 (tttm) REVERT: C 448 ASN cc_start: 0.8062 (t0) cc_final: 0.7394 (m-40) REVERT: C 646 ARG cc_start: 0.7145 (mmm160) cc_final: 0.6856 (mmp80) REVERT: C 740 MET cc_start: 0.7237 (ppp) cc_final: 0.6699 (ppp) REVERT: C 900 MET cc_start: 0.2970 (mmm) cc_final: 0.2235 (mmm) REVERT: C 964 LYS cc_start: 0.8350 (tptp) cc_final: 0.7979 (tppp) REVERT: C 1007 TYR cc_start: 0.7558 (t80) cc_final: 0.6895 (t80) REVERT: C 1038 LYS cc_start: 0.8351 (mmtm) cc_final: 0.8090 (mmtm) REVERT: C 1145 LEU cc_start: 0.3184 (OUTLIER) cc_final: 0.2865 (tt) outliers start: 187 outliers final: 172 residues processed: 574 average time/residue: 0.9234 time to fit residues: 812.2174 Evaluate side-chains 607 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 426 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 2.9990 chunk 311 optimal weight: 0.6980 chunk 190 optimal weight: 0.1980 chunk 147 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 326 optimal weight: 30.0000 chunk 300 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 26919 Z= 0.359 Angle : 1.394 59.152 36614 Z= 0.728 Chirality : 0.240 1.807 4254 Planarity : 0.005 0.071 4684 Dihedral : 9.898 179.560 4558 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 35.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.66 % Favored : 90.25 % Rotamer: Outliers : 6.68 % Allowed : 29.97 % Favored : 63.35 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.14), residues: 3245 helix: -0.65 (0.19), residues: 660 sheet: -1.38 (0.20), residues: 637 loop : -2.23 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.132 0.003 TRP A 64 HIS 0.008 0.002 HIS B 66 PHE 0.021 0.002 PHE A 43 TYR 0.022 0.002 TYR C 37 ARG 0.006 0.001 ARG B1014 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 428 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7230 (t80) cc_final: 0.6810 (t80) REVERT: A 129 LYS cc_start: 0.8783 (mttt) cc_final: 0.8359 (mmtt) REVERT: A 207 HIS cc_start: 0.6520 (p-80) cc_final: 0.6225 (p-80) REVERT: A 301 CYS cc_start: 0.7693 (p) cc_final: 0.7479 (p) REVERT: A 368 LEU cc_start: 0.2469 (OUTLIER) cc_final: 0.1367 (tp) REVERT: A 952 VAL cc_start: 0.8603 (m) cc_final: 0.8222 (t) REVERT: A 1094 VAL cc_start: 0.6032 (OUTLIER) cc_final: 0.5523 (t) REVERT: A 1103 PHE cc_start: 0.5119 (m-80) cc_final: 0.3583 (m-80) REVERT: B 64 TRP cc_start: 0.6333 (t-100) cc_final: 0.5902 (t-100) REVERT: B 374 PHE cc_start: 0.2808 (OUTLIER) cc_final: -0.1298 (m-80) REVERT: B 455 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.5192 (mp) REVERT: B 456 PHE cc_start: 0.3604 (OUTLIER) cc_final: 0.2055 (m-80) REVERT: B 613 GLN cc_start: 0.6864 (tp40) cc_final: 0.6139 (tm-30) REVERT: B 735 SER cc_start: 0.7244 (OUTLIER) cc_final: 0.6513 (p) REVERT: B 902 MET cc_start: 0.7050 (ttp) cc_final: 0.6493 (ttp) REVERT: B 983 ARG cc_start: 0.8081 (tmm-80) cc_final: 0.7605 (tmm-80) REVERT: C 160 TYR cc_start: 0.6487 (p90) cc_final: 0.5938 (p90) REVERT: C 177 MET cc_start: 0.1718 (mtm) cc_final: 0.1404 (mtm) REVERT: C 444 LYS cc_start: 0.3723 (OUTLIER) cc_final: 0.1038 (tttm) REVERT: C 448 ASN cc_start: 0.8056 (t0) cc_final: 0.7387 (m-40) REVERT: C 646 ARG cc_start: 0.7139 (mmm160) cc_final: 0.6855 (mmp80) REVERT: C 740 MET cc_start: 0.7232 (ppp) cc_final: 0.6690 (ppp) REVERT: C 900 MET cc_start: 0.2961 (mmm) cc_final: 0.2229 (mmm) REVERT: C 964 LYS cc_start: 0.8357 (tptp) cc_final: 0.7983 (tppp) REVERT: C 1007 TYR cc_start: 0.7553 (t80) cc_final: 0.6890 (t80) REVERT: C 1038 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8087 (mmtm) REVERT: C 1145 LEU cc_start: 0.3182 (OUTLIER) cc_final: 0.2862 (tt) outliers start: 189 outliers final: 178 residues processed: 565 average time/residue: 0.9425 time to fit residues: 817.3999 Evaluate side-chains 613 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 427 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 239 optimal weight: 0.2980 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 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 = 0.4394 r_free = 0.4394 target = 0.148490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.110449 restraints weight = 224570.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.117664 restraints weight = 124065.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.122800 restraints weight = 76944.199| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4098 r_free = 0.4098 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4098 r_free = 0.4098 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 26919 Z= 0.359 Angle : 1.394 59.152 36614 Z= 0.728 Chirality : 0.240 1.807 4254 Planarity : 0.005 0.071 4684 Dihedral : 9.898 179.560 4558 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 35.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.66 % Favored : 90.25 % Rotamer: Outliers : 6.57 % Allowed : 29.97 % Favored : 63.46 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.14), residues: 3245 helix: -0.65 (0.19), residues: 660 sheet: -1.38 (0.20), residues: 637 loop : -2.23 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.132 0.003 TRP A 64 HIS 0.008 0.002 HIS B 66 PHE 0.021 0.002 PHE A 43 TYR 0.022 0.002 TYR C 37 ARG 0.006 0.001 ARG B1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14606.15 seconds wall clock time: 258 minutes 36.20 seconds (15516.20 seconds total)