Starting phenix.real_space_refine on Fri Jul 26 18:09:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xob_33343/07_2024/7xob_33343_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xob_33343/07_2024/7xob_33343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xob_33343/07_2024/7xob_33343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xob_33343/07_2024/7xob_33343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xob_33343/07_2024/7xob_33343_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xob_33343/07_2024/7xob_33343_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 Zn 2 6.06 5 S 163 5.16 5 C 21781 2.51 5 N 5634 2.21 5 O 6528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E ARG 340": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "E GLU 398": "OE1" <-> "OE2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E GLU 489": "OE1" <-> "OE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E ARG 577": "NH1" <-> "NH2" Residue "E ARG 600": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 34108 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 7938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7938 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 55, 'TRANS': 968} Chain breaks: 8 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "C" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 19.09, per 1000 atoms: 0.56 Number of scatterers: 34108 At special positions: 0 Unit cell: (159.032, 140.08, 247.2, 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) Zn 2 29.99 S 163 16.00 O 6528 8.00 N 5634 7.00 C 21781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.32 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.65 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 D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 122 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B1098 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C 331 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 53 " " NAG E 902 " - " ASN E 546 " " NAG E 903 " - " ASN E 53 " Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 5.5 seconds 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8006 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 51 sheets defined 35.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.689A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.883A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.503A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 3.864A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.690A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.013A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.629A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.553A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.508A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) 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 543 through 546 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.975A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 778 removed outlier: 3.953A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.711A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.020A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.066A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.834A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.588A pdb=" N ASN D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.599A pdb=" N LEU D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.771A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.253A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.614A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 219 through 232 removed outlier: 4.068A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.349A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.207A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.641A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.656A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.220A pdb=" N ARG D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.596A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.700A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.813A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.275A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.698A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.591A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.575A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.835A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.626A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.904A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.883A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.503A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 778 removed outlier: 3.865A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.690A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.014A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.062A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.628A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.554A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.589A pdb=" N ASN E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.598A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.771A pdb=" N ALA E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.253A pdb=" N ALA E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.615A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 219 through 232 removed outlier: 4.068A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 4.349A pdb=" N ASP E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 256 removed outlier: 4.208A pdb=" N ILE E 256 " --> pdb=" O PRO E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.641A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.655A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 removed outlier: 4.221A pdb=" N ARG E 387 " --> pdb=" O ALA E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 3.596A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.700A pdb=" N LYS E 419 " --> pdb=" O PRO E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.812A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.276A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 532 removed outlier: 3.699A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.591A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.576A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.836A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.626A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.645A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.157A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.798A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 4.339A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.757A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.617A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.625A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.085A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.074A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.639A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.415A 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: 3.767A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.981A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.719A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.700A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.101A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 126 through 132 removed outlier: 4.166A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 189 through 194 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.666A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.104A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.663A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.946A pdb=" N TYR B 453 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.840A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.764A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.765A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.869A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.675A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.000A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.644A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.157A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.798A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 171 through 172 removed outlier: 4.339A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.756A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.552A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.617A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.085A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 714 removed outlier: 3.639A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.767A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.675A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.000A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 347 through 350 1335 hydrogen bonds defined for protein. 3699 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: 13.19 Time building geometry restraints manager: 13.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5912 1.32 - 1.46: 11401 1.46 - 1.59: 17399 1.59 - 1.73: 0 1.73 - 1.86: 229 Bond restraints: 34941 Sorted by residual: bond pdb=" CA SER A 555 " pdb=" CB SER A 555 " ideal model delta sigma weight residual 1.532 1.450 0.081 1.56e-02 4.11e+03 2.73e+01 bond pdb=" CA SER C 555 " pdb=" CB SER C 555 " ideal model delta sigma weight residual 1.530 1.453 0.077 1.69e-02 3.50e+03 2.06e+01 bond pdb=" CA THR C 866 " pdb=" C THR C 866 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.39e-02 5.18e+03 1.74e+01 bond pdb=" CA THR A 866 " pdb=" C THR A 866 " ideal model delta sigma weight residual 1.528 1.471 0.058 1.39e-02 5.18e+03 1.72e+01 bond pdb=" CA SER A 530 " pdb=" CB SER A 530 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.34e-02 5.57e+03 1.71e+01 ... (remaining 34936 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.85: 871 105.85 - 112.91: 18176 112.91 - 119.97: 12208 119.97 - 127.03: 15867 127.03 - 134.10: 410 Bond angle restraints: 47532 Sorted by residual: angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 112.17 101.34 10.83 9.50e-01 1.11e+00 1.30e+02 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 121.97 -11.27 1.22e+00 6.72e-01 8.54e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 121.96 -11.26 1.22e+00 6.72e-01 8.51e+01 angle pdb=" O ALA B 372 " pdb=" C ALA B 372 " pdb=" N PRO B 373 " ideal model delta sigma weight residual 120.48 112.39 8.09 8.90e-01 1.26e+00 8.26e+01 angle pdb=" N ILE A 569 " pdb=" CA ILE A 569 " pdb=" C ILE A 569 " ideal model delta sigma weight residual 111.81 104.21 7.60 8.60e-01 1.35e+00 7.82e+01 ... (remaining 47527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.67: 19808 20.67 - 41.35: 1139 41.35 - 62.02: 210 62.02 - 82.69: 37 82.69 - 103.37: 32 Dihedral angle restraints: 21226 sinusoidal: 8790 harmonic: 12436 Sorted by residual: dihedral pdb=" CB CYS E 344 " pdb=" SG CYS E 344 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -170.71 84.71 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -170.71 84.71 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -163.39 77.39 1 1.00e+01 1.00e-02 7.50e+01 ... (remaining 21223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 5298 0.261 - 0.523: 62 0.523 - 0.784: 10 0.784 - 1.045: 2 1.045 - 1.307: 2 Chirality restraints: 5374 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.27e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.22e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 5371 not shown) Planarity restraints: 6135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " -0.332 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B1309 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " 0.508 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " 0.321 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG B1310 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " 0.117 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.320 2.00e-02 2.50e+03 2.77e-01 9.61e+02 pdb=" C7 NAG A1304 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.203 2.00e-02 2.50e+03 ... (remaining 6132 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 3 2.04 - 2.76: 4707 2.76 - 3.47: 46669 3.47 - 4.19: 80006 4.19 - 4.90: 140348 Nonbonded interactions: 271733 Sorted by model distance: nonbonded pdb=" O VAL B 367 " pdb=" CE2 PHE B 371 " model vdw 1.329 3.340 nonbonded pdb=" CA CYS B 131 " pdb=" SG CYS B 166 " model vdw 1.977 3.064 nonbonded pdb=" O ASN C 657 " pdb=" OD1 ASN C 657 " model vdw 1.981 3.040 nonbonded pdb=" O PHE A 562 " pdb=" CE LYS C 41 " model vdw 2.047 3.440 nonbonded pdb=" O THR B 124 " pdb=" OD1 ASN B 125 " model vdw 2.075 3.040 ... (remaining 271728 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 27 through 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 464 or (resid 465 and (name N or name CA or name C or name O or name CB \ )) or resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 520 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 1146 or resid 1301 through 1311)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 464 or (resid 465 and (name N or name CA or name C or name O or name CB \ )) or resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 520 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 1146 or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.460 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 86.290 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.140 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4163 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34941 Z= 0.335 Angle : 0.916 11.641 47532 Z= 0.588 Chirality : 0.076 1.307 5374 Planarity : 0.013 0.286 6098 Dihedral : 13.732 103.368 13100 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.95 % Rotamer: Outliers : 0.57 % Allowed : 10.12 % Favored : 89.31 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.11), residues: 4202 helix: -0.73 (0.13), residues: 1370 sheet: -1.70 (0.18), residues: 613 loop : -3.11 (0.11), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 104 HIS 0.008 0.001 HIS B 207 PHE 0.069 0.002 PHE B 92 TYR 0.062 0.001 TYR B 37 ARG 0.017 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 894 time to evaluate : 3.493 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: A 328 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7455 (mmm160) REVERT: A 543 PHE cc_start: 0.8287 (m-10) cc_final: 0.7970 (m-80) REVERT: A 547 THR cc_start: 0.8006 (p) cc_final: 0.7793 (p) REVERT: A 551 VAL cc_start: 0.8022 (t) cc_final: 0.7689 (m) REVERT: A 569 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8170 (tp) REVERT: A 610 VAL cc_start: 0.7896 (t) cc_final: 0.7653 (t) REVERT: A 692 ILE cc_start: 0.7976 (mm) cc_final: 0.7656 (mt) REVERT: A 737 ASP cc_start: 0.6872 (t0) cc_final: 0.6151 (t70) REVERT: A 774 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7236 (mp10) REVERT: A 819 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 820 ASP cc_start: 0.6815 (t0) cc_final: 0.6583 (t0) REVERT: A 821 LEU cc_start: 0.8767 (tt) cc_final: 0.8556 (tp) REVERT: A 929 SER cc_start: 0.8426 (t) cc_final: 0.8153 (m) REVERT: A 934 ILE cc_start: 0.7936 (tt) cc_final: 0.7706 (tt) REVERT: A 949 GLN cc_start: 0.7729 (tp40) cc_final: 0.7512 (mm-40) REVERT: A 1019 ARG cc_start: 0.6932 (ttm110) cc_final: 0.6450 (ttp80) REVERT: A 1091 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6964 (mtt90) REVERT: A 1122 VAL cc_start: 0.8323 (p) cc_final: 0.8045 (m) REVERT: A 1136 THR cc_start: 0.7856 (t) cc_final: 0.7571 (p) REVERT: B 36 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7625 (p) REVERT: B 308 VAL cc_start: 0.7264 (m) cc_final: 0.5992 (t) REVERT: B 309 GLU cc_start: 0.6944 (mp0) cc_final: 0.6695 (mp0) REVERT: B 317 ASN cc_start: 0.7161 (m110) cc_final: 0.6594 (m110) REVERT: B 340 GLU cc_start: 0.7219 (tp30) cc_final: 0.6665 (tp30) REVERT: B 615 VAL cc_start: 0.8265 (p) cc_final: 0.8032 (p) REVERT: B 645 THR cc_start: 0.8366 (p) cc_final: 0.7167 (m) REVERT: B 670 ILE cc_start: 0.7990 (mp) cc_final: 0.7762 (mt) REVERT: B 698 SER cc_start: 0.8261 (t) cc_final: 0.7860 (p) REVERT: B 774 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7236 (mp10) REVERT: B 981 LEU cc_start: 0.7542 (mm) cc_final: 0.7166 (mm) REVERT: B 994 ASP cc_start: 0.7474 (t0) cc_final: 0.7096 (t0) REVERT: D 39 LEU cc_start: 0.4606 (mt) cc_final: 0.4352 (mt) REVERT: D 334 THR cc_start: 0.3953 (t) cc_final: 0.3626 (p) REVERT: C 44 ARG cc_start: 0.7744 (mtt180) cc_final: 0.6853 (mtt180) REVERT: C 309 GLU cc_start: 0.5827 (mm-30) cc_final: 0.5547 (mm-30) REVERT: C 329 PHE cc_start: 0.7600 (m-80) cc_final: 0.7367 (m-80) REVERT: C 542 ASN cc_start: 0.7841 (t0) cc_final: 0.7402 (t0) REVERT: C 567 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7960 (ptp-170) REVERT: C 584 ILE cc_start: 0.7905 (tp) cc_final: 0.7571 (mm) REVERT: C 644 GLN cc_start: 0.7003 (tp40) cc_final: 0.6736 (tp40) REVERT: C 655 TYR cc_start: 0.7618 (t80) cc_final: 0.7305 (t80) REVERT: C 772 VAL cc_start: 0.8023 (p) cc_final: 0.7723 (m) REVERT: C 816 SER cc_start: 0.8499 (p) cc_final: 0.8298 (p) REVERT: C 819 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7385 (mt-10) REVERT: C 1018 ILE cc_start: 0.7030 (mm) cc_final: 0.6806 (mm) REVERT: C 1128 VAL cc_start: 0.8708 (m) cc_final: 0.8499 (p) outliers start: 21 outliers final: 2 residues processed: 908 average time/residue: 0.4764 time to fit residues: 693.8682 Evaluate side-chains 742 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 737 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 567 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 178 optimal weight: 0.0770 chunk 109 optimal weight: 0.9980 chunk 216 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 332 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 202 optimal weight: 0.0170 chunk 247 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 188 ASN A 394 ASN A 405 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 755 GLN A 935 GLN A 949 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1005 GLN A1106 GLN A1135 ASN B 81 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 606 ASN B 613 GLN B 804 GLN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 965 GLN B1106 GLN D 98 GLN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS C 125 ASN C 188 ASN C 314 GLN C 405 ASN C 563 GLN C 613 GLN C 755 GLN C 787 GLN C 895 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C 978 ASN E 42 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 113 ASN E 188 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 HIS E 368 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4396 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34941 Z= 0.214 Angle : 0.603 10.474 47532 Z= 0.302 Chirality : 0.045 0.536 5374 Planarity : 0.004 0.052 6098 Dihedral : 6.504 106.456 5363 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.60 % Allowed : 15.17 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.12), residues: 4202 helix: 0.39 (0.15), residues: 1355 sheet: -1.07 (0.20), residues: 584 loop : -2.55 (0.11), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 258 HIS 0.006 0.001 HIS D 322 PHE 0.035 0.002 PHE B 371 TYR 0.020 0.001 TYR C1138 ARG 0.007 0.001 ARG E 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 793 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 541 PHE cc_start: 0.7744 (p90) cc_final: 0.7433 (p90) REVERT: A 555 SER cc_start: 0.7309 (p) cc_final: 0.7072 (t) REVERT: A 586 ASP cc_start: 0.6499 (m-30) cc_final: 0.6252 (m-30) REVERT: A 737 ASP cc_start: 0.6896 (t0) cc_final: 0.6347 (t0) REVERT: A 781 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.6108 (t) REVERT: A 790 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7586 (mtmm) REVERT: A 819 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6900 (mt-10) REVERT: A 921 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7531 (ttmm) REVERT: A 929 SER cc_start: 0.8516 (t) cc_final: 0.8271 (m) REVERT: A 934 ILE cc_start: 0.8257 (tt) cc_final: 0.7954 (tp) REVERT: A 1136 THR cc_start: 0.8091 (t) cc_final: 0.7775 (p) REVERT: B 29 THR cc_start: 0.6520 (t) cc_final: 0.4950 (p) REVERT: B 317 ASN cc_start: 0.7386 (m110) cc_final: 0.6864 (m110) REVERT: B 340 GLU cc_start: 0.7332 (tp30) cc_final: 0.6768 (tp30) REVERT: B 347 PHE cc_start: 0.6664 (m-80) cc_final: 0.5913 (m-10) REVERT: B 361 CYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6932 (p) REVERT: B 380 TYR cc_start: 0.7314 (m-80) cc_final: 0.7045 (m-10) REVERT: B 515 PHE cc_start: 0.7118 (m-10) cc_final: 0.6687 (m-80) REVERT: B 651 ILE cc_start: 0.8129 (pt) cc_final: 0.7722 (mt) REVERT: B 658 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7074 (p0) REVERT: B 698 SER cc_start: 0.8459 (t) cc_final: 0.8079 (p) REVERT: B 774 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7370 (mp10) REVERT: B 1091 ARG cc_start: 0.7532 (mtt90) cc_final: 0.7151 (mtt180) REVERT: B 1103 PHE cc_start: 0.8029 (m-80) cc_final: 0.7828 (m-10) REVERT: B 1127 ASP cc_start: 0.7041 (t0) cc_final: 0.6710 (t0) REVERT: D 325 GLN cc_start: 0.3528 (mp10) cc_final: 0.3325 (mp10) REVERT: D 334 THR cc_start: 0.4288 (t) cc_final: 0.3605 (p) REVERT: D 385 TYR cc_start: 0.3778 (p90) cc_final: 0.3561 (p90) REVERT: D 444 LEU cc_start: 0.0898 (mt) cc_final: 0.0185 (mm) REVERT: C 317 ASN cc_start: 0.7511 (m-40) cc_final: 0.7181 (m-40) REVERT: C 329 PHE cc_start: 0.7999 (m-80) cc_final: 0.7798 (m-80) REVERT: C 542 ASN cc_start: 0.7940 (t0) cc_final: 0.7436 (t0) REVERT: C 655 TYR cc_start: 0.7810 (t80) cc_final: 0.7463 (t80) REVERT: C 772 VAL cc_start: 0.8250 (p) cc_final: 0.7975 (m) REVERT: C 1029 MET cc_start: 0.7964 (tpp) cc_final: 0.7555 (ttm) REVERT: C 1128 VAL cc_start: 0.8707 (m) cc_final: 0.8466 (p) REVERT: E 249 MET cc_start: 0.1071 (mmt) cc_final: 0.0711 (mmt) outliers start: 96 outliers final: 36 residues processed: 843 average time/residue: 0.4473 time to fit residues: 604.8315 Evaluate side-chains 770 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 731 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 320 optimal weight: 1.9990 chunk 262 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 385 optimal weight: 0.9990 chunk 416 optimal weight: 6.9990 chunk 343 optimal weight: 0.9990 chunk 382 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 309 optimal weight: 0.0970 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 784 GLN B1135 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 373 HIS D 472 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN E 30 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 96 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4598 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34941 Z= 0.279 Angle : 0.634 11.346 47532 Z= 0.323 Chirality : 0.047 0.544 5374 Planarity : 0.004 0.053 6098 Dihedral : 5.525 101.646 5354 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 3.50 % Allowed : 17.85 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4202 helix: 0.55 (0.15), residues: 1390 sheet: -0.77 (0.19), residues: 603 loop : -2.30 (0.12), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 203 HIS 0.010 0.001 HIS B1064 PHE 0.027 0.002 PHE B 201 TYR 0.024 0.002 TYR A1110 ARG 0.008 0.001 ARG E 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 815 time to evaluate : 3.603 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: A 120 VAL cc_start: 0.7771 (m) cc_final: 0.7552 (p) REVERT: A 302 THR cc_start: 0.8366 (m) cc_final: 0.8106 (t) REVERT: A 576 VAL cc_start: 0.8565 (p) cc_final: 0.8352 (t) REVERT: A 595 VAL cc_start: 0.8667 (m) cc_final: 0.8445 (t) REVERT: A 615 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7474 (p) REVERT: A 710 ASN cc_start: 0.7745 (p0) cc_final: 0.7511 (p0) REVERT: A 756 TYR cc_start: 0.8083 (m-80) cc_final: 0.7731 (m-80) REVERT: A 790 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7632 (mtmm) REVERT: A 819 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 820 ASP cc_start: 0.6950 (t0) cc_final: 0.6695 (m-30) REVERT: A 934 ILE cc_start: 0.8626 (tt) cc_final: 0.8183 (tp) REVERT: A 1003 SER cc_start: 0.8882 (p) cc_final: 0.8670 (t) REVERT: A 1105 THR cc_start: 0.8071 (t) cc_final: 0.7848 (p) REVERT: B 40 ASP cc_start: 0.7794 (m-30) cc_final: 0.7536 (m-30) REVERT: B 317 ASN cc_start: 0.7396 (m110) cc_final: 0.7146 (m110) REVERT: B 340 GLU cc_start: 0.7546 (tp30) cc_final: 0.7074 (tp30) REVERT: B 380 TYR cc_start: 0.7565 (m-80) cc_final: 0.7256 (m-10) REVERT: B 396 TYR cc_start: 0.7473 (m-80) cc_final: 0.7254 (m-80) REVERT: B 425 LEU cc_start: 0.7977 (mp) cc_final: 0.7694 (mt) REVERT: B 471 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6437 (mt-10) REVERT: B 525 CYS cc_start: 0.7478 (m) cc_final: 0.6706 (m) REVERT: B 619 GLU cc_start: 0.6496 (mp0) cc_final: 0.6149 (mp0) REVERT: B 644 GLN cc_start: 0.7584 (tp40) cc_final: 0.7280 (tp40) REVERT: B 651 ILE cc_start: 0.8259 (pt) cc_final: 0.7959 (mt) REVERT: B 658 ASN cc_start: 0.7564 (p0) cc_final: 0.7148 (p0) REVERT: B 698 SER cc_start: 0.8758 (t) cc_final: 0.8419 (p) REVERT: B 710 ASN cc_start: 0.7857 (p0) cc_final: 0.7612 (p0) REVERT: B 719 THR cc_start: 0.8444 (t) cc_final: 0.8133 (p) REVERT: B 730 SER cc_start: 0.8501 (p) cc_final: 0.8252 (t) REVERT: B 774 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7429 (mp10) REVERT: B 781 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7752 (t) REVERT: B 821 LEU cc_start: 0.8335 (tp) cc_final: 0.8034 (tt) REVERT: B 934 ILE cc_start: 0.8184 (tt) cc_final: 0.7966 (tt) REVERT: B 1073 LYS cc_start: 0.7736 (mtpt) cc_final: 0.7470 (mtpp) REVERT: B 1104 VAL cc_start: 0.8690 (t) cc_final: 0.8367 (p) REVERT: B 1127 ASP cc_start: 0.7258 (t0) cc_final: 0.6910 (t0) REVERT: D 246 ARG cc_start: 0.1658 (mmm160) cc_final: 0.0710 (mmt180) REVERT: D 334 THR cc_start: 0.4353 (t) cc_final: 0.3704 (p) REVERT: C 190 ARG cc_start: 0.4988 (mtt180) cc_final: 0.4161 (mtt180) REVERT: C 307 THR cc_start: 0.7515 (p) cc_final: 0.7209 (p) REVERT: C 317 ASN cc_start: 0.7435 (m-40) cc_final: 0.7186 (m-40) REVERT: C 542 ASN cc_start: 0.7890 (t0) cc_final: 0.7293 (t0) REVERT: C 673 SER cc_start: 0.8510 (p) cc_final: 0.8286 (t) REVERT: C 708 SER cc_start: 0.8145 (m) cc_final: 0.7737 (p) REVERT: C 710 ASN cc_start: 0.7449 (p0) cc_final: 0.7197 (p0) REVERT: C 718 PHE cc_start: 0.7689 (p90) cc_final: 0.7448 (p90) REVERT: C 820 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: C 1128 VAL cc_start: 0.8679 (m) cc_final: 0.8390 (p) REVERT: C 1136 THR cc_start: 0.8365 (t) cc_final: 0.7895 (p) outliers start: 129 outliers final: 73 residues processed: 891 average time/residue: 0.4472 time to fit residues: 647.7545 Evaluate side-chains 830 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 754 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 184 optimal weight: 0.2980 chunk 259 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 chunk 409 optimal weight: 6.9990 chunk 202 optimal weight: 0.3980 chunk 366 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 925 ASN A 949 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 540 ASN B 784 GLN B 919 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 787 GLN C 919 ASN C 935 GLN C1054 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN E 239 HIS E 322 HIS ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4629 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34941 Z= 0.219 Angle : 0.575 8.888 47532 Z= 0.292 Chirality : 0.045 0.512 5374 Planarity : 0.004 0.055 6098 Dihedral : 5.225 89.421 5354 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.58 % Allowed : 19.05 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4202 helix: 0.80 (0.15), residues: 1387 sheet: -0.63 (0.19), residues: 623 loop : -2.10 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 461 HIS 0.006 0.001 HIS C1101 PHE 0.028 0.002 PHE A 377 TYR 0.017 0.001 TYR B 369 ARG 0.008 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 769 time to evaluate : 3.841 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: A 302 THR cc_start: 0.8295 (m) cc_final: 0.8066 (t) REVERT: A 585 LEU cc_start: 0.8470 (mt) cc_final: 0.8204 (mt) REVERT: A 615 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7604 (p) REVERT: A 710 ASN cc_start: 0.7856 (p0) cc_final: 0.7637 (p0) REVERT: A 737 ASP cc_start: 0.6927 (t0) cc_final: 0.6329 (t0) REVERT: A 756 TYR cc_start: 0.8163 (m-80) cc_final: 0.7914 (m-80) REVERT: A 781 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8053 (t) REVERT: A 790 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7684 (mtmm) REVERT: A 820 ASP cc_start: 0.6851 (t0) cc_final: 0.6570 (m-30) REVERT: A 934 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8216 (tp) REVERT: B 29 THR cc_start: 0.7150 (t) cc_final: 0.5441 (p) REVERT: B 40 ASP cc_start: 0.7841 (m-30) cc_final: 0.7610 (m-30) REVERT: B 317 ASN cc_start: 0.7521 (m110) cc_final: 0.6827 (m110) REVERT: B 340 GLU cc_start: 0.7608 (tp30) cc_final: 0.7136 (tp30) REVERT: B 347 PHE cc_start: 0.6718 (m-10) cc_final: 0.6459 (m-10) REVERT: B 361 CYS cc_start: 0.7899 (OUTLIER) cc_final: 0.6953 (p) REVERT: B 398 ASP cc_start: 0.7898 (m-30) cc_final: 0.7543 (m-30) REVERT: B 471 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6550 (mt-10) REVERT: B 543 PHE cc_start: 0.7458 (m-80) cc_final: 0.7161 (m-80) REVERT: B 644 GLN cc_start: 0.7500 (tp40) cc_final: 0.7187 (tp40) REVERT: B 658 ASN cc_start: 0.7574 (p0) cc_final: 0.7180 (p0) REVERT: B 698 SER cc_start: 0.8733 (t) cc_final: 0.8395 (p) REVERT: B 710 ASN cc_start: 0.7936 (p0) cc_final: 0.7665 (p0) REVERT: B 719 THR cc_start: 0.8468 (t) cc_final: 0.8173 (p) REVERT: B 730 SER cc_start: 0.8532 (p) cc_final: 0.8255 (t) REVERT: B 774 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7433 (mp10) REVERT: B 821 LEU cc_start: 0.8249 (tp) cc_final: 0.7991 (tt) REVERT: B 934 ILE cc_start: 0.8245 (tt) cc_final: 0.7896 (tt) REVERT: B 1127 ASP cc_start: 0.7307 (t0) cc_final: 0.7012 (t0) REVERT: D 75 GLU cc_start: 0.1400 (mt-10) cc_final: 0.0944 (mt-10) REVERT: D 322 HIS cc_start: 0.2017 (OUTLIER) cc_final: 0.1486 (m90) REVERT: D 334 THR cc_start: 0.4397 (t) cc_final: 0.3511 (p) REVERT: D 571 GLU cc_start: 0.2701 (tm-30) cc_final: 0.2421 (tm-30) REVERT: C 307 THR cc_start: 0.7722 (p) cc_final: 0.7465 (p) REVERT: C 317 ASN cc_start: 0.7405 (m-40) cc_final: 0.7140 (m-40) REVERT: C 339 ASP cc_start: 0.6566 (p0) cc_final: 0.6251 (p0) REVERT: C 539 VAL cc_start: 0.7737 (m) cc_final: 0.7506 (m) REVERT: C 542 ASN cc_start: 0.7857 (t0) cc_final: 0.7370 (t0) REVERT: C 708 SER cc_start: 0.8111 (m) cc_final: 0.7737 (p) REVERT: C 710 ASN cc_start: 0.7500 (p0) cc_final: 0.7267 (p0) REVERT: C 718 PHE cc_start: 0.8080 (p90) cc_final: 0.7743 (p90) REVERT: C 781 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7670 (t) REVERT: C 1128 VAL cc_start: 0.8642 (m) cc_final: 0.8366 (p) REVERT: C 1136 THR cc_start: 0.8332 (t) cc_final: 0.7943 (p) REVERT: E 332 MET cc_start: 0.0372 (ptm) cc_final: 0.0029 (ptp) outliers start: 132 outliers final: 82 residues processed: 838 average time/residue: 0.4482 time to fit residues: 606.4755 Evaluate side-chains 833 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 745 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 283 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 367 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1005 GLN B 125 ASN B 901 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS D 373 HIS D 586 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 901 GLN C 935 GLN C 954 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN E 24 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN E 417 HIS ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4767 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 34941 Z= 0.399 Angle : 0.687 12.369 47532 Z= 0.355 Chirality : 0.049 0.514 5374 Planarity : 0.005 0.059 6098 Dihedral : 5.524 83.577 5354 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.53 % Allowed : 19.32 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 4202 helix: 0.56 (0.14), residues: 1409 sheet: -0.58 (0.18), residues: 662 loop : -2.01 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 461 HIS 0.010 0.001 HIS E 401 PHE 0.029 0.002 PHE B 275 TYR 0.023 0.002 TYR C 756 ARG 0.011 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 812 time to evaluate : 3.805 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: A 41 LYS cc_start: 0.5363 (ttmt) cc_final: 0.4630 (mtpt) REVERT: A 80 ASP cc_start: 0.5567 (OUTLIER) cc_final: 0.4360 (m-30) REVERT: A 204 TYR cc_start: 0.6947 (m-80) cc_final: 0.6675 (m-80) REVERT: A 240 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7479 (t) REVERT: A 585 LEU cc_start: 0.8498 (mt) cc_final: 0.8245 (mt) REVERT: A 595 VAL cc_start: 0.8656 (m) cc_final: 0.8442 (t) REVERT: A 710 ASN cc_start: 0.8171 (p0) cc_final: 0.7964 (p0) REVERT: A 737 ASP cc_start: 0.6632 (t0) cc_final: 0.6320 (t0) REVERT: A 756 TYR cc_start: 0.8378 (m-80) cc_final: 0.8143 (m-80) REVERT: A 790 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7648 (mtpt) REVERT: A 820 ASP cc_start: 0.6829 (t0) cc_final: 0.6628 (m-30) REVERT: A 934 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8523 (tp) REVERT: A 994 ASP cc_start: 0.7250 (t0) cc_final: 0.6798 (t0) REVERT: A 1104 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 1120 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8054 (p) REVERT: A 1135 ASN cc_start: 0.7960 (t0) cc_final: 0.7723 (t0) REVERT: B 118 LEU cc_start: 0.7389 (pp) cc_final: 0.6899 (pp) REVERT: B 196 ASN cc_start: 0.7905 (t0) cc_final: 0.7687 (t0) REVERT: B 291 CYS cc_start: 0.5898 (m) cc_final: 0.5428 (m) REVERT: B 298 GLU cc_start: 0.6826 (tp30) cc_final: 0.6478 (tp30) REVERT: B 317 ASN cc_start: 0.7386 (m110) cc_final: 0.6972 (m-40) REVERT: B 340 GLU cc_start: 0.7756 (tp30) cc_final: 0.7336 (tp30) REVERT: B 398 ASP cc_start: 0.7866 (m-30) cc_final: 0.7480 (m-30) REVERT: B 414 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7043 (mp10) REVERT: B 453 TYR cc_start: 0.7289 (p90) cc_final: 0.6721 (p90) REVERT: B 543 PHE cc_start: 0.7738 (m-80) cc_final: 0.7468 (m-80) REVERT: B 552 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7670 (mt) REVERT: B 651 ILE cc_start: 0.8257 (pt) cc_final: 0.8001 (mp) REVERT: B 658 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7214 (p0) REVERT: B 698 SER cc_start: 0.8766 (t) cc_final: 0.8445 (p) REVERT: B 710 ASN cc_start: 0.8147 (p0) cc_final: 0.7828 (p0) REVERT: B 719 THR cc_start: 0.8471 (t) cc_final: 0.8222 (p) REVERT: B 730 SER cc_start: 0.8502 (p) cc_final: 0.8245 (t) REVERT: B 747 THR cc_start: 0.7961 (p) cc_final: 0.7354 (m) REVERT: B 751 ASN cc_start: 0.8038 (m-40) cc_final: 0.7763 (m-40) REVERT: B 781 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7922 (t) REVERT: B 821 LEU cc_start: 0.8224 (tp) cc_final: 0.8024 (tt) REVERT: B 825 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7694 (mttm) REVERT: B 969 LYS cc_start: 0.8264 (ptpt) cc_final: 0.8023 (ptpp) REVERT: B 1017 GLU cc_start: 0.6882 (tp30) cc_final: 0.6612 (tp30) REVERT: B 1128 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8490 (p) REVERT: D 101 GLN cc_start: 0.4231 (tt0) cc_final: 0.2870 (mt0) REVERT: D 334 THR cc_start: 0.4284 (t) cc_final: 0.3639 (p) REVERT: C 317 ASN cc_start: 0.7381 (m-40) cc_final: 0.7136 (m-40) REVERT: C 584 ILE cc_start: 0.8100 (tp) cc_final: 0.7871 (mm) REVERT: C 708 SER cc_start: 0.8212 (m) cc_final: 0.7884 (p) REVERT: C 723 THR cc_start: 0.8207 (m) cc_final: 0.7870 (p) REVERT: C 964 LYS cc_start: 0.8021 (tppp) cc_final: 0.7752 (tptp) REVERT: C 1128 VAL cc_start: 0.8592 (m) cc_final: 0.8335 (p) REVERT: C 1136 THR cc_start: 0.8436 (t) cc_final: 0.8071 (p) REVERT: E 183 TYR cc_start: 0.1958 (OUTLIER) cc_final: 0.0586 (t80) outliers start: 167 outliers final: 99 residues processed: 905 average time/residue: 0.4589 time to fit residues: 672.4732 Evaluate side-chains 865 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 756 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 2.9990 chunk 369 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 410 optimal weight: 9.9990 chunk 340 optimal weight: 0.5980 chunk 189 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 215 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 613 GLN B 901 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 562 ASN C 505 HIS C 607 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 925 ASN C 949 GLN C1054 GLN E 30 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4733 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34941 Z= 0.223 Angle : 0.626 11.093 47532 Z= 0.318 Chirality : 0.045 0.391 5374 Planarity : 0.004 0.056 6098 Dihedral : 5.750 95.409 5354 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.72 % Allowed : 21.60 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4202 helix: 0.75 (0.14), residues: 1407 sheet: -0.32 (0.19), residues: 636 loop : -1.92 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 461 HIS 0.005 0.001 HIS A 207 PHE 0.024 0.002 PHE B 201 TYR 0.025 0.001 TYR E 207 ARG 0.007 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 764 time to evaluate : 3.399 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: A 204 TYR cc_start: 0.6891 (m-80) cc_final: 0.6605 (m-80) REVERT: A 227 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6459 (t) REVERT: A 239 GLN cc_start: 0.7245 (mp10) cc_final: 0.6767 (mp10) REVERT: A 585 LEU cc_start: 0.8423 (mt) cc_final: 0.8137 (mt) REVERT: A 790 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7471 (mtmm) REVERT: A 934 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8470 (tp) REVERT: A 1005 GLN cc_start: 0.7249 (mt0) cc_final: 0.7040 (mt0) REVERT: A 1084 ASP cc_start: 0.7499 (t0) cc_final: 0.6976 (t0) REVERT: A 1120 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8032 (p) REVERT: A 1135 ASN cc_start: 0.7896 (t0) cc_final: 0.7653 (t0) REVERT: A 1136 THR cc_start: 0.8455 (t) cc_final: 0.8206 (p) REVERT: B 237 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6185 (mmt180) REVERT: B 317 ASN cc_start: 0.7604 (m110) cc_final: 0.7122 (m110) REVERT: B 340 GLU cc_start: 0.7724 (tp30) cc_final: 0.7333 (tp30) REVERT: B 386 LYS cc_start: 0.7717 (mmtp) cc_final: 0.7509 (mttt) REVERT: B 398 ASP cc_start: 0.7766 (m-30) cc_final: 0.7273 (m-30) REVERT: B 414 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7075 (mp10) REVERT: B 430 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8475 (p) REVERT: B 543 PHE cc_start: 0.7844 (m-80) cc_final: 0.7505 (m-80) REVERT: B 651 ILE cc_start: 0.8229 (pt) cc_final: 0.7972 (mp) REVERT: B 658 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7307 (p0) REVERT: B 698 SER cc_start: 0.8767 (t) cc_final: 0.8400 (p) REVERT: B 710 ASN cc_start: 0.8113 (p0) cc_final: 0.7798 (p0) REVERT: B 719 THR cc_start: 0.8463 (t) cc_final: 0.8256 (p) REVERT: B 730 SER cc_start: 0.8503 (p) cc_final: 0.8249 (t) REVERT: B 747 THR cc_start: 0.7905 (p) cc_final: 0.7373 (m) REVERT: B 751 ASN cc_start: 0.8033 (m-40) cc_final: 0.7726 (m-40) REVERT: B 781 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7806 (t) REVERT: B 804 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7514 (mm-40) REVERT: B 821 LEU cc_start: 0.8113 (tp) cc_final: 0.7891 (tt) REVERT: B 969 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7945 (ptpp) REVERT: B 1017 GLU cc_start: 0.6886 (tp30) cc_final: 0.6679 (tp30) REVERT: D 75 GLU cc_start: 0.1382 (mt-10) cc_final: 0.1166 (mt-10) REVERT: D 101 GLN cc_start: 0.4277 (tt0) cc_final: 0.2871 (mt0) REVERT: D 458 LYS cc_start: 0.0540 (mmtm) cc_final: 0.0174 (mmtm) REVERT: C 317 ASN cc_start: 0.7447 (m-40) cc_final: 0.7155 (m-40) REVERT: C 327 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 535 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8362 (mttp) REVERT: C 708 SER cc_start: 0.8120 (m) cc_final: 0.7768 (p) REVERT: C 723 THR cc_start: 0.8225 (m) cc_final: 0.7865 (p) REVERT: C 821 LEU cc_start: 0.8440 (tp) cc_final: 0.8136 (tt) REVERT: C 1128 VAL cc_start: 0.8570 (m) cc_final: 0.8315 (p) REVERT: C 1136 THR cc_start: 0.8384 (t) cc_final: 0.8063 (p) REVERT: E 183 TYR cc_start: 0.2238 (OUTLIER) cc_final: 0.1711 (t80) outliers start: 137 outliers final: 91 residues processed: 839 average time/residue: 0.4646 time to fit residues: 627.6657 Evaluate side-chains 829 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 728 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 552 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 233 optimal weight: 0.0570 chunk 299 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 408 optimal weight: 0.9980 chunk 255 optimal weight: 0.5980 chunk 249 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B1088 HIS ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN C 69 HIS C 607 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4798 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34941 Z= 0.348 Angle : 0.682 18.328 47532 Z= 0.348 Chirality : 0.048 0.392 5374 Planarity : 0.005 0.059 6098 Dihedral : 5.737 79.066 5354 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.96 % Allowed : 21.73 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4202 helix: 0.65 (0.14), residues: 1417 sheet: -0.23 (0.19), residues: 642 loop : -1.87 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 461 HIS 0.007 0.001 HIS C1064 PHE 0.053 0.002 PHE D 308 TYR 0.028 0.002 TYR C 453 ARG 0.009 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 779 time to evaluate : 3.602 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: A 41 LYS cc_start: 0.5641 (ttmt) cc_final: 0.5251 (mttt) REVERT: A 204 TYR cc_start: 0.7023 (m-80) cc_final: 0.6698 (m-80) REVERT: A 537 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7242 (ptmt) REVERT: A 583 GLU cc_start: 0.7054 (tp30) cc_final: 0.6438 (tp30) REVERT: A 934 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8525 (tp) REVERT: A 994 ASP cc_start: 0.6971 (t0) cc_final: 0.6745 (t0) REVERT: A 1084 ASP cc_start: 0.7605 (t0) cc_final: 0.7138 (t0) REVERT: A 1127 ASP cc_start: 0.6879 (t0) cc_final: 0.6653 (t0) REVERT: A 1135 ASN cc_start: 0.7903 (t0) cc_final: 0.7651 (t0) REVERT: A 1136 THR cc_start: 0.8464 (t) cc_final: 0.8223 (p) REVERT: B 237 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6073 (mmp-170) REVERT: B 340 GLU cc_start: 0.7790 (tp30) cc_final: 0.7459 (tp30) REVERT: B 398 ASP cc_start: 0.7741 (m-30) cc_final: 0.7333 (m-30) REVERT: B 414 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7369 (mp10) REVERT: B 430 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8486 (p) REVERT: B 462 LYS cc_start: 0.8303 (mmmm) cc_final: 0.7891 (mmmm) REVERT: B 463 PRO cc_start: 0.8645 (Cg_exo) cc_final: 0.8284 (Cg_endo) REVERT: B 658 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7316 (p0) REVERT: B 698 SER cc_start: 0.8780 (t) cc_final: 0.8431 (p) REVERT: B 710 ASN cc_start: 0.8206 (p0) cc_final: 0.7866 (p0) REVERT: B 730 SER cc_start: 0.8508 (p) cc_final: 0.8174 (m) REVERT: B 747 THR cc_start: 0.7931 (p) cc_final: 0.7334 (m) REVERT: B 751 ASN cc_start: 0.8042 (m-40) cc_final: 0.7772 (m-40) REVERT: B 781 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7856 (t) REVERT: B 825 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7849 (mmtp) REVERT: B 907 ASN cc_start: 0.7937 (t0) cc_final: 0.7570 (t0) REVERT: B 950 ASP cc_start: 0.7108 (m-30) cc_final: 0.6851 (m-30) REVERT: B 1017 GLU cc_start: 0.6888 (tp30) cc_final: 0.6643 (tp30) REVERT: D 101 GLN cc_start: 0.4089 (tt0) cc_final: 0.2858 (mt0) REVERT: D 230 PHE cc_start: 0.5663 (OUTLIER) cc_final: 0.4345 (m-80) REVERT: C 281 GLU cc_start: 0.6621 (pm20) cc_final: 0.6385 (pm20) REVERT: C 317 ASN cc_start: 0.7489 (m-40) cc_final: 0.7170 (m-40) REVERT: C 535 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8441 (mttp) REVERT: C 644 GLN cc_start: 0.6718 (tp40) cc_final: 0.6459 (tt0) REVERT: C 691 SER cc_start: 0.8558 (p) cc_final: 0.8261 (m) REVERT: C 708 SER cc_start: 0.8160 (m) cc_final: 0.7824 (p) REVERT: C 723 THR cc_start: 0.8217 (m) cc_final: 0.7880 (p) REVERT: C 821 LEU cc_start: 0.8477 (tp) cc_final: 0.8178 (tt) REVERT: C 1128 VAL cc_start: 0.8584 (m) cc_final: 0.8316 (p) REVERT: C 1136 THR cc_start: 0.8436 (t) cc_final: 0.8103 (p) REVERT: E 183 TYR cc_start: 0.2268 (OUTLIER) cc_final: 0.1671 (t80) REVERT: E 190 MET cc_start: 0.1172 (mtt) cc_final: 0.0277 (ppp) REVERT: E 556 LYS cc_start: 0.0578 (mmtm) cc_final: -0.0045 (tppp) outliers start: 146 outliers final: 106 residues processed: 861 average time/residue: 0.4836 time to fit residues: 676.7717 Evaluate side-chains 863 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 749 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 552 GLN Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 0.9980 chunk 163 optimal weight: 0.5980 chunk 244 optimal weight: 30.0000 chunk 123 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 259 optimal weight: 10.0000 chunk 278 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 321 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN D 24 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN C 207 HIS C 388 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 949 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4772 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34941 Z= 0.235 Angle : 0.654 19.567 47532 Z= 0.330 Chirality : 0.046 0.544 5374 Planarity : 0.004 0.060 6098 Dihedral : 5.654 89.011 5354 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.34 % Rotamer: Outliers : 3.66 % Allowed : 22.25 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4202 helix: 0.74 (0.14), residues: 1417 sheet: -0.28 (0.19), residues: 629 loop : -1.74 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 461 HIS 0.004 0.001 HIS E 345 PHE 0.029 0.002 PHE D 308 TYR 0.026 0.002 TYR E 41 ARG 0.012 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 766 time to evaluate : 3.693 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: A 204 TYR cc_start: 0.6944 (m-80) cc_final: 0.6678 (m-80) REVERT: A 537 LYS cc_start: 0.7616 (ttmt) cc_final: 0.7190 (ptmt) REVERT: A 554 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6375 (mm-30) REVERT: A 576 VAL cc_start: 0.8630 (p) cc_final: 0.8418 (t) REVERT: A 583 GLU cc_start: 0.6899 (tp30) cc_final: 0.6675 (tp30) REVERT: A 934 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8506 (tp) REVERT: A 1005 GLN cc_start: 0.7287 (mt0) cc_final: 0.7066 (mt0) REVERT: A 1084 ASP cc_start: 0.7569 (t0) cc_final: 0.7045 (t0) REVERT: A 1127 ASP cc_start: 0.6878 (t0) cc_final: 0.6569 (t0) REVERT: A 1135 ASN cc_start: 0.7885 (t0) cc_final: 0.7625 (t0) REVERT: A 1136 THR cc_start: 0.8442 (t) cc_final: 0.8225 (p) REVERT: B 237 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6100 (mmp-170) REVERT: B 317 ASN cc_start: 0.7607 (m110) cc_final: 0.7201 (m-40) REVERT: B 340 GLU cc_start: 0.7738 (tp30) cc_final: 0.7432 (tp30) REVERT: B 398 ASP cc_start: 0.7687 (m-30) cc_final: 0.7401 (m-30) REVERT: B 399 SER cc_start: 0.8203 (t) cc_final: 0.7963 (p) REVERT: B 414 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7290 (mp10) REVERT: B 430 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8443 (p) REVERT: B 462 LYS cc_start: 0.8266 (mmmm) cc_final: 0.7862 (mmmm) REVERT: B 463 PRO cc_start: 0.8646 (Cg_exo) cc_final: 0.8286 (Cg_endo) REVERT: B 471 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7052 (mt-10) REVERT: B 651 ILE cc_start: 0.8194 (pt) cc_final: 0.7955 (mp) REVERT: B 658 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7304 (p0) REVERT: B 698 SER cc_start: 0.8734 (t) cc_final: 0.8371 (p) REVERT: B 710 ASN cc_start: 0.8213 (p0) cc_final: 0.7871 (p0) REVERT: B 730 SER cc_start: 0.8514 (p) cc_final: 0.8183 (m) REVERT: B 747 THR cc_start: 0.7921 (p) cc_final: 0.7299 (m) REVERT: B 751 ASN cc_start: 0.8038 (m-40) cc_final: 0.7746 (m-40) REVERT: B 781 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7811 (t) REVERT: B 804 GLN cc_start: 0.7855 (mm110) cc_final: 0.7650 (mm-40) REVERT: B 825 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7835 (mmtp) REVERT: B 907 ASN cc_start: 0.7935 (t0) cc_final: 0.7550 (t0) REVERT: B 933 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7978 (mtpt) REVERT: B 950 ASP cc_start: 0.7057 (m-30) cc_final: 0.6765 (m-30) REVERT: B 1017 GLU cc_start: 0.6878 (tp30) cc_final: 0.6667 (tp30) REVERT: D 101 GLN cc_start: 0.4286 (tt0) cc_final: 0.3281 (mt0) REVERT: D 230 PHE cc_start: 0.5824 (OUTLIER) cc_final: 0.4854 (m-80) REVERT: C 88 ASP cc_start: 0.5940 (t0) cc_final: 0.5622 (t0) REVERT: C 281 GLU cc_start: 0.6618 (pm20) cc_final: 0.6388 (pm20) REVERT: C 317 ASN cc_start: 0.7506 (m-40) cc_final: 0.7190 (m-40) REVERT: C 327 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8401 (p) REVERT: C 535 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8412 (mttp) REVERT: C 542 ASN cc_start: 0.7838 (t0) cc_final: 0.7363 (t0) REVERT: C 691 SER cc_start: 0.8556 (p) cc_final: 0.8259 (m) REVERT: C 708 SER cc_start: 0.8092 (m) cc_final: 0.7767 (p) REVERT: C 723 THR cc_start: 0.8227 (m) cc_final: 0.7872 (p) REVERT: C 821 LEU cc_start: 0.8437 (tp) cc_final: 0.8144 (tt) REVERT: C 1128 VAL cc_start: 0.8579 (m) cc_final: 0.8301 (p) REVERT: C 1136 THR cc_start: 0.8387 (t) cc_final: 0.8094 (p) REVERT: E 183 TYR cc_start: 0.2282 (OUTLIER) cc_final: 0.1682 (t80) REVERT: E 556 LYS cc_start: 0.0818 (mmtm) cc_final: 0.0285 (tppp) REVERT: E 567 THR cc_start: 0.2340 (p) cc_final: 0.1993 (t) outliers start: 135 outliers final: 98 residues processed: 847 average time/residue: 0.4687 time to fit residues: 635.6334 Evaluate side-chains 861 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 754 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 473 TRP Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 552 GLN Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 0.9980 chunk 391 optimal weight: 0.7980 chunk 357 optimal weight: 0.0870 chunk 380 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 165 optimal weight: 0.4980 chunk 299 optimal weight: 0.0060 chunk 116 optimal weight: 1.9990 chunk 344 optimal weight: 1.9990 chunk 360 optimal weight: 0.8980 chunk 379 optimal weight: 20.0000 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN D 24 ASN D 42 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4763 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34941 Z= 0.204 Angle : 0.639 19.792 47532 Z= 0.322 Chirality : 0.045 0.344 5374 Planarity : 0.004 0.060 6098 Dihedral : 5.555 97.046 5354 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 3.42 % Allowed : 22.73 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 4202 helix: 0.79 (0.14), residues: 1417 sheet: -0.25 (0.19), residues: 637 loop : -1.66 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP D 461 HIS 0.004 0.001 HIS E 345 PHE 0.027 0.001 PHE D 308 TYR 0.027 0.001 TYR D 237 ARG 0.008 0.000 ARG E 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 762 time to evaluate : 3.820 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: A 204 TYR cc_start: 0.6961 (m-80) cc_final: 0.6634 (m-80) REVERT: A 537 LYS cc_start: 0.7566 (ttmt) cc_final: 0.7108 (ptmt) REVERT: A 554 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6314 (mm-30) REVERT: A 583 GLU cc_start: 0.6914 (tp30) cc_final: 0.6661 (tp30) REVERT: A 934 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 1084 ASP cc_start: 0.7562 (t0) cc_final: 0.7013 (t0) REVERT: A 1127 ASP cc_start: 0.6864 (t0) cc_final: 0.6534 (t0) REVERT: A 1135 ASN cc_start: 0.7881 (t0) cc_final: 0.7616 (t0) REVERT: A 1136 THR cc_start: 0.8460 (t) cc_final: 0.8246 (p) REVERT: B 317 ASN cc_start: 0.7587 (m110) cc_final: 0.7236 (m-40) REVERT: B 340 GLU cc_start: 0.7689 (tp30) cc_final: 0.7434 (tp30) REVERT: B 354 ASN cc_start: 0.7844 (t0) cc_final: 0.7576 (t0) REVERT: B 398 ASP cc_start: 0.7701 (m-30) cc_final: 0.7433 (m-30) REVERT: B 414 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7246 (mp10) REVERT: B 430 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 462 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7826 (mmmm) REVERT: B 463 PRO cc_start: 0.8629 (Cg_exo) cc_final: 0.8249 (Cg_endo) REVERT: B 471 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 515 PHE cc_start: 0.8124 (m-80) cc_final: 0.7841 (m-10) REVERT: B 651 ILE cc_start: 0.8169 (pt) cc_final: 0.7926 (mp) REVERT: B 710 ASN cc_start: 0.8173 (p0) cc_final: 0.7861 (p0) REVERT: B 730 SER cc_start: 0.8542 (p) cc_final: 0.8219 (t) REVERT: B 747 THR cc_start: 0.7885 (p) cc_final: 0.7351 (m) REVERT: B 751 ASN cc_start: 0.8037 (m-40) cc_final: 0.7746 (m-40) REVERT: B 781 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7777 (t) REVERT: B 825 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7819 (mmtp) REVERT: B 907 ASN cc_start: 0.7936 (t0) cc_final: 0.7550 (t0) REVERT: B 933 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7978 (mtpt) REVERT: B 950 ASP cc_start: 0.7015 (m-30) cc_final: 0.6685 (m-30) REVERT: D 95 ARG cc_start: 0.3549 (ttp-110) cc_final: 0.3196 (ttm110) REVERT: D 101 GLN cc_start: 0.4334 (tt0) cc_final: 0.3239 (mt0) REVERT: D 230 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.4932 (m-80) REVERT: D 458 LYS cc_start: 0.1049 (mmtt) cc_final: 0.0845 (mmtt) REVERT: C 88 ASP cc_start: 0.5993 (t0) cc_final: 0.5644 (t0) REVERT: C 317 ASN cc_start: 0.7475 (m-40) cc_final: 0.7198 (m-40) REVERT: C 327 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8417 (p) REVERT: C 542 ASN cc_start: 0.7847 (t0) cc_final: 0.7434 (t0) REVERT: C 691 SER cc_start: 0.8551 (p) cc_final: 0.8232 (m) REVERT: C 708 SER cc_start: 0.8069 (m) cc_final: 0.7738 (p) REVERT: C 723 THR cc_start: 0.8184 (m) cc_final: 0.7805 (p) REVERT: C 781 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7651 (t) REVERT: C 821 LEU cc_start: 0.8437 (tp) cc_final: 0.8150 (tt) REVERT: C 1128 VAL cc_start: 0.8568 (m) cc_final: 0.8313 (p) REVERT: C 1136 THR cc_start: 0.8392 (t) cc_final: 0.8110 (p) REVERT: E 183 TYR cc_start: 0.2310 (OUTLIER) cc_final: 0.1830 (t80) REVERT: E 556 LYS cc_start: 0.1113 (mmtm) cc_final: 0.0609 (tppp) REVERT: E 567 THR cc_start: 0.2247 (p) cc_final: 0.1879 (t) outliers start: 126 outliers final: 103 residues processed: 836 average time/residue: 0.4663 time to fit residues: 625.6102 Evaluate side-chains 857 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 747 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 552 GLN Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 20.0000 chunk 402 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 191 optimal weight: 0.6980 chunk 279 optimal weight: 0.9990 chunk 422 optimal weight: 20.0000 chunk 388 optimal weight: 0.6980 chunk 336 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 368 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 34941 Z= 0.569 Angle : 0.801 20.938 47532 Z= 0.412 Chirality : 0.053 0.637 5374 Planarity : 0.005 0.055 6098 Dihedral : 6.216 107.648 5354 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.76 % Favored : 93.22 % Rotamer: Outliers : 3.42 % Allowed : 23.11 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 4202 helix: 0.45 (0.14), residues: 1421 sheet: -0.27 (0.19), residues: 637 loop : -1.86 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP D 461 HIS 0.011 0.002 HIS A1064 PHE 0.041 0.003 PHE B 392 TYR 0.033 0.003 TYR D 454 ARG 0.011 0.001 ARG D 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8404 Ramachandran restraints generated. 4202 Oldfield, 0 Emsley, 4202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 814 time to evaluate : 4.231 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: A 48 LEU cc_start: 0.8156 (mm) cc_final: 0.7926 (mp) REVERT: A 196 ASN cc_start: 0.6660 (p0) cc_final: 0.6307 (p0) REVERT: A 204 TYR cc_start: 0.7022 (m-80) cc_final: 0.6717 (m-80) REVERT: A 588 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7927 (p) REVERT: A 719 THR cc_start: 0.8531 (t) cc_final: 0.8227 (p) REVERT: A 994 ASP cc_start: 0.7098 (t0) cc_final: 0.6807 (t0) REVERT: A 995 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7513 (mtm-85) REVERT: A 1084 ASP cc_start: 0.7701 (t0) cc_final: 0.7327 (t0) REVERT: A 1127 ASP cc_start: 0.7011 (t0) cc_final: 0.6651 (t0) REVERT: A 1135 ASN cc_start: 0.7880 (t0) cc_final: 0.7624 (t0) REVERT: A 1136 THR cc_start: 0.8514 (t) cc_final: 0.8301 (p) REVERT: B 298 GLU cc_start: 0.6848 (tp30) cc_final: 0.6566 (tp30) REVERT: B 317 ASN cc_start: 0.7488 (m110) cc_final: 0.7133 (m-40) REVERT: B 340 GLU cc_start: 0.7756 (tp30) cc_final: 0.7554 (tp30) REVERT: B 398 ASP cc_start: 0.7891 (m-30) cc_final: 0.7571 (m-30) REVERT: B 430 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8498 (p) REVERT: B 462 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8000 (mmmm) REVERT: B 651 ILE cc_start: 0.8257 (pt) cc_final: 0.7924 (mt) REVERT: B 710 ASN cc_start: 0.8362 (p0) cc_final: 0.7943 (p0) REVERT: B 730 SER cc_start: 0.8543 (p) cc_final: 0.8182 (m) REVERT: B 747 THR cc_start: 0.7989 (p) cc_final: 0.7353 (m) REVERT: B 751 ASN cc_start: 0.8089 (m-40) cc_final: 0.7804 (m-40) REVERT: B 781 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7953 (t) REVERT: B 907 ASN cc_start: 0.8014 (t0) cc_final: 0.7640 (t0) REVERT: B 933 LYS cc_start: 0.8275 (ttpp) cc_final: 0.8064 (mtpt) REVERT: D 101 GLN cc_start: 0.4464 (tt0) cc_final: 0.3555 (tt0) REVERT: D 230 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5426 (m-80) REVERT: D 332 MET cc_start: 0.0774 (ptt) cc_final: 0.0499 (ptt) REVERT: D 450 LEU cc_start: 0.2721 (tp) cc_final: 0.2027 (tp) REVERT: D 481 LYS cc_start: 0.1545 (ptmm) cc_final: 0.1132 (tttm) REVERT: C 88 ASP cc_start: 0.6360 (t0) cc_final: 0.6134 (m-30) REVERT: C 317 ASN cc_start: 0.7593 (m-40) cc_final: 0.7262 (m-40) REVERT: C 535 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8527 (mttp) REVERT: C 644 GLN cc_start: 0.6827 (tp40) cc_final: 0.6494 (tt0) REVERT: C 691 SER cc_start: 0.8571 (p) cc_final: 0.8317 (m) REVERT: C 708 SER cc_start: 0.8190 (m) cc_final: 0.7880 (p) REVERT: C 723 THR cc_start: 0.8181 (m) cc_final: 0.7872 (p) REVERT: C 781 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7787 (t) REVERT: C 821 LEU cc_start: 0.8525 (tp) cc_final: 0.8205 (tt) REVERT: C 977 LEU cc_start: 0.8329 (mm) cc_final: 0.8114 (mt) REVERT: C 982 SER cc_start: 0.7473 (p) cc_final: 0.6943 (m) REVERT: C 993 ILE cc_start: 0.8328 (mm) cc_final: 0.8101 (mt) REVERT: C 1128 VAL cc_start: 0.8596 (m) cc_final: 0.8321 (p) REVERT: C 1136 THR cc_start: 0.8505 (t) cc_final: 0.8191 (p) REVERT: E 183 TYR cc_start: 0.2547 (OUTLIER) cc_final: 0.1921 (t80) REVERT: E 190 MET cc_start: 0.2126 (mtt) cc_final: 0.1577 (mtt) REVERT: E 203 TRP cc_start: 0.3997 (OUTLIER) cc_final: 0.2759 (t-100) REVERT: E 556 LYS cc_start: 0.1401 (mmtm) cc_final: 0.0687 (tppp) REVERT: E 567 THR cc_start: 0.2787 (p) cc_final: 0.2201 (t) outliers start: 126 outliers final: 92 residues processed: 884 average time/residue: 0.4692 time to fit residues: 663.3166 Evaluate side-chains 889 residues out of total 3722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 790 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 552 GLN Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 3.9990 chunk 358 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 310 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 93 optimal weight: 0.2980 chunk 336 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 345 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B 49 HIS B 414 GLN B 540 ASN B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.200325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146483 restraints weight = 53633.682| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.72 r_work: 0.3564 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34941 Z= 0.239 Angle : 0.676 20.552 47532 Z= 0.344 Chirality : 0.047 0.637 5374 Planarity : 0.004 0.058 6098 Dihedral : 5.813 94.980 5354 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 2.88 % Allowed : 24.28 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4202 helix: 0.67 (0.14), residues: 1420 sheet: -0.30 (0.19), residues: 647 loop : -1.70 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP D 461 HIS 0.005 0.001 HIS C1101 PHE 0.032 0.002 PHE A 823 TYR 0.036 0.002 TYR D 454 ARG 0.012 0.001 ARG D 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11634.27 seconds wall clock time: 205 minutes 5.20 seconds (12305.20 seconds total)