Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 15 09:53:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpa_32680/10_2023/7wpa_32680_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpa_32680/10_2023/7wpa_32680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpa_32680/10_2023/7wpa_32680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpa_32680/10_2023/7wpa_32680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpa_32680/10_2023/7wpa_32680_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpa_32680/10_2023/7wpa_32680_neut.pdb" } resolution = 2.77 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= 0.021 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 142 5.16 5 Cl 1 4.86 5 C 19446 2.51 5 N 5000 2.21 5 O 5854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 643": "NH1" <-> "NH2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 812": "NH1" <-> "NH2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A ARG 902": "NH1" <-> "NH2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "A ARG 1016": "NH1" <-> "NH2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B ARG 506": "NH1" <-> "NH2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B ARG 631": "NH1" <-> "NH2" Residue "B ARG 643": "NH1" <-> "NH2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B ARG 762": "NH1" <-> "NH2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B ARG 812": "NH1" <-> "NH2" Residue "B ARG 844": "NH1" <-> "NH2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B ARG 902": "NH1" <-> "NH2" Residue "B GLU 915": "OE1" <-> "OE2" Residue "B ARG 980": "NH1" <-> "NH2" Residue "B ARG 992": "NH1" <-> "NH2" Residue "B ARG 997": "NH1" <-> "NH2" Residue "B ARG 1011": "NH1" <-> "NH2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "B ARG 1016": "NH1" <-> "NH2" Residue "B GLU 1028": "OE1" <-> "OE2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B ARG 1088": "NH1" <-> "NH2" Residue "B ARG 1104": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C ARG 316": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C ARG 343": "NH1" <-> "NH2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 495": "NH1" <-> "NH2" Residue "C ARG 506": "NH1" <-> "NH2" Residue "C ARG 564": "NH1" <-> "NH2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C ARG 631": "NH1" <-> "NH2" Residue "C ARG 643": "NH1" <-> "NH2" Residue "C ARG 762": "NH1" <-> "NH2" Residue "C ARG 812": "NH1" <-> "NH2" Residue "C ARG 844": "NH1" <-> "NH2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 980": "NH1" <-> "NH2" Residue "C ARG 992": "NH1" <-> "NH2" Residue "C ARG 997": "NH1" <-> "NH2" Residue "C ARG 1011": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C ARG 1088": "NH1" <-> "NH2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C GLU 1141": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 393": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D ARG 482": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D ARG 582": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 30444 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8329 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 56, 'TRANS': 1004} Chain breaks: 6 Chain: "B" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8329 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 56, 'TRANS': 1004} Chain breaks: 6 Chain: "C" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8297 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 56, 'TRANS': 1000} Chain breaks: 8 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 14.86, per 1000 atoms: 0.49 Number of scatterers: 30444 At special positions: 0 Unit cell: (126.896, 139.256, 244.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 142 16.00 O 5854 8.00 N 5000 7.00 C 19446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 279 " " NAG A1302 " - " ASN A 613 " " NAG A1303 " - " ASN A 706 " " NAG A1304 " - " ASN A1071 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 714 " " NAG B1301 " - " ASN B 279 " " NAG B1302 " - " ASN B 613 " " NAG B1303 " - " ASN B 706 " " NAG B1304 " - " ASN B1071 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 714 " " NAG C1301 " - " ASN C 279 " " NAG C1302 " - " ASN C 613 " " NAG C1303 " - " ASN C 706 " " NAG C1304 " - " ASN C1071 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 714 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 546 " " NAG E 1 " - " ASN A 328 " " NAG F 1 " - " ASN A 798 " " NAG G 1 " - " ASN A1131 " " NAG H 1 " - " ASN A1095 " " NAG I 1 " - " ASN B 328 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1131 " " NAG L 1 " - " ASN B1095 " " NAG M 1 " - " ASN C 328 " " NAG N 1 " - " ASN C 798 " " NAG O 1 " - " ASN C1131 " " NAG P 1 " - " ASN C1095 " Time building additional restraints: 11.38 Conformation dependent library (CDL) restraints added in 3.8 seconds 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7112 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 50 sheets defined 25.1% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.621A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.638A pdb=" N ALA A 623 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.506A pdb=" N TYR A 753 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.572A pdb=" N GLN A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 removed outlier: 3.732A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.872A pdb=" N ALA A 849 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 846 through 851' Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.560A pdb=" N THR A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.564A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.608A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.613A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.504A pdb=" N LYS A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.856A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 974 through 979 removed outlier: 4.490A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 979 " --> pdb=" O ASN A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 979' Processing helix chain 'A' and resid 982 through 1029 removed outlier: 3.659A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.092A pdb=" N SER A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.886A pdb=" N LEU B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 381 through 387 removed outlier: 3.820A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 387' Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.111A pdb=" N HIS B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 623 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 624 " --> pdb=" O ILE B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 624' Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.238A pdb=" N LEU B 750 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 751 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 754 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.784A pdb=" N ALA B 763 " --> pdb=" O GLN B 759 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 822 Processing helix chain 'B' and resid 845 through 852 Processing helix chain 'B' and resid 863 through 882 removed outlier: 3.692A pdb=" N THR B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.962A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 905 " --> pdb=" O TYR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.633A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 916 " --> pdb=" O VAL B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 910 through 916' Processing helix chain 'B' and resid 916 through 936 removed outlier: 3.661A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.946A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.565A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 3.744A pdb=" N GLU B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 995 " --> pdb=" O ASP B 991 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.867A pdb=" N LEU C 368 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.567A pdb=" N GLN C 406 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 620 through 627 removed outlier: 3.803A pdb=" N ASP C 624 " --> pdb=" O ILE C 621 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 627 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.638A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 779 removed outlier: 3.649A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 removed outlier: 4.047A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 853 removed outlier: 3.722A pdb=" N ALA C 849 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN C 850 " --> pdb=" O ILE C 847 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 851 " --> pdb=" O CYS C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 879 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.502A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 removed outlier: 3.624A pdb=" N ASN C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 905 " --> pdb=" O TYR C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.575A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 removed outlier: 3.523A pdb=" N LYS C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 961 removed outlier: 4.072A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.682A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.577A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.544A pdb=" N SER C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.929A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 67 removed outlier: 3.817A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 77 removed outlier: 4.795A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 98 removed outlier: 3.695A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 110 through 125 removed outlier: 3.639A pdb=" N THR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 removed outlier: 4.198A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 removed outlier: 4.699A pdb=" N GLU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 186 removed outlier: 4.253A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D 184 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.631A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.884A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 228 through 232 removed outlier: 4.071A pdb=" N GLU D 232 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.747A pdb=" N GLU D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.590A pdb=" N LEU D 278 " --> pdb=" O TRP D 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 275 through 279' Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.775A pdb=" N ALA D 296 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET D 297 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.758A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 383 removed outlier: 4.259A pdb=" N THR D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 408 removed outlier: 3.755A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.730A pdb=" N TYR D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 removed outlier: 3.767A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 479 through 484' Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.589A pdb=" N LEU D 503 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 521 No H-bonds generated for 'chain 'D' and resid 519 through 521' Processing helix chain 'D' and resid 522 through 527 Processing helix chain 'D' and resid 528 through 531 removed outlier: 4.249A pdb=" N GLN D 531 " --> pdb=" O ALA D 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 528 through 531' Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 554 through 559 removed outlier: 3.853A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 554 through 559' Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 588 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.683A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 91 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 186 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 190 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 197 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.869A pdb=" N PHE A 43 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 583 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.869A pdb=" N PHE A 43 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 583 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.344A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.616A pdb=" N LEU A 82 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 127 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 124 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 167 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.930A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.750A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 394 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 535 through 540 removed outlier: 3.659A pdb=" N GLY A 545 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 657 removed outlier: 5.003A pdb=" N THR A 693 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN A 655 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 698 through 701 removed outlier: 6.375A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS C 787 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN A 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.899A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.899A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.268A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 784 through 786 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.490A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.535A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 264 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 186 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE B 196 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP B 225 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE B 198 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 221 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.901A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.629A pdb=" N ARG B 234 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 114 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 129 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.857A pdb=" N GLY B 590 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 315 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AC8, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.593A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 432 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 373 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 470 through 471 removed outlier: 4.027A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.257A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 688 " --> pdb=" O GLN B 672 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 672 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 663 " --> pdb=" O ILE B 667 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 714 through 725 removed outlier: 7.539A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.422A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 784 through 787 removed outlier: 6.063A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1117 through 1119 removed outlier: 3.769A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.775A pdb=" N GLU C 186 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 201 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.513A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AE3, first strand: chain 'C' and resid 114 through 119 removed outlier: 3.839A pdb=" N SER C 167 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.604A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.809A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN C 539 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C 547 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 582 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 573 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE7, first strand: chain 'C' and resid 395 through 399 removed outlier: 3.745A pdb=" N PHE C 397 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 449 through 450 Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.056A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 688 " --> pdb=" O GLN C 672 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.546A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 722 " --> pdb=" O PHE C1059 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.546A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 722 " --> pdb=" O PHE C1059 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.345A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF5, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.853A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2466 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: 13.00 Time building geometry restraints manager: 12.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5057 1.32 - 1.45: 8649 1.45 - 1.57: 17265 1.57 - 1.70: 0 1.70 - 1.82: 190 Bond restraints: 31161 Sorted by residual: bond pdb=" C ARG D 582 " pdb=" N PRO D 583 " ideal model delta sigma weight residual 1.337 1.379 -0.043 9.80e-03 1.04e+04 1.91e+01 bond pdb=" C PRO B 983 " pdb=" O PRO B 983 " ideal model delta sigma weight residual 1.240 1.196 0.045 1.12e-02 7.97e+03 1.59e+01 bond pdb=" C GLN C1139 " pdb=" N PRO C1140 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.36e-02 5.41e+03 1.35e+01 bond pdb=" C PRO A 983 " pdb=" O PRO A 983 " ideal model delta sigma weight residual 1.240 1.209 0.032 1.12e-02 7.97e+03 8.00e+00 bond pdb=" CA ALA A 986 " pdb=" CB ALA A 986 " ideal model delta sigma weight residual 1.528 1.485 0.044 1.59e-02 3.96e+03 7.49e+00 ... (remaining 31156 not shown) Histogram of bond angle deviations from ideal: 100.36 - 109.01: 2154 109.01 - 117.65: 20654 117.65 - 126.30: 19135 126.30 - 134.94: 442 134.94 - 143.58: 1 Bond angle restraints: 42386 Sorted by residual: angle pdb=" N PRO C 983 " pdb=" CA PRO C 983 " pdb=" C PRO C 983 " ideal model delta sigma weight residual 110.70 122.80 -12.10 1.22e+00 6.72e-01 9.83e+01 angle pdb=" C LEU A 458 " pdb=" N LYS A 459 " pdb=" CA LYS A 459 " ideal model delta sigma weight residual 122.21 143.58 -21.37 2.87e+00 1.21e-01 5.55e+01 angle pdb=" N VAL C 619 " pdb=" CA VAL C 619 " pdb=" C VAL C 619 " ideal model delta sigma weight residual 111.77 104.70 7.07 1.04e+00 9.25e-01 4.62e+01 angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 118.98 -8.28 1.22e+00 6.72e-01 4.60e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 120.79 129.08 -8.29 1.39e+00 5.18e-01 3.55e+01 ... (remaining 42381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 16337 17.71 - 35.42: 1440 35.42 - 53.13: 303 53.13 - 70.85: 56 70.85 - 88.56: 32 Dihedral angle restraints: 18168 sinusoidal: 7137 harmonic: 11031 Sorted by residual: dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 2.56 -88.56 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1123 " pdb=" CB CYS B1123 " ideal model delta sinusoidal sigma weight residual -86.00 -14.28 -71.72 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CB CYS A 477 " pdb=" SG CYS A 477 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 159.87 -66.87 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 18165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4759 0.118 - 0.237: 114 0.237 - 0.355: 1 0.355 - 0.473: 3 0.473 - 0.591: 2 Chirality restraints: 4879 Sorted by residual: chirality pdb=" CA PRO C 983 " pdb=" N PRO C 983 " pdb=" C PRO C 983 " pdb=" CB PRO C 983 " both_signs ideal model delta sigma weight residual False 2.72 2.13 0.59 2.00e-01 2.50e+01 8.74e+00 chirality pdb=" CA PRO B 983 " pdb=" N PRO B 983 " pdb=" C PRO B 983 " pdb=" CB PRO B 983 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 4876 not shown) Planarity restraints: 5454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1139 " -0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO A1140 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A1140 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1140 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 980 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.15e+00 pdb=" C ARG C 980 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG C 980 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 981 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 980 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.34e+00 pdb=" C ARG A 980 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG A 980 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 981 " -0.016 2.00e-02 2.50e+03 ... (remaining 5451 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 9801 2.84 - 3.36: 24303 3.36 - 3.87: 49610 3.87 - 4.39: 54868 4.39 - 4.90: 95187 Nonbonded interactions: 233769 Sorted by model distance: nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 216 " model vdw 2.327 2.440 nonbonded pdb=" OG SER A 881 " pdb=" OG1 THR A 884 " model vdw 2.329 2.440 nonbonded pdb=" O SER A 940 " pdb=" OG SER A 940 " model vdw 2.331 2.440 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 216 " model vdw 2.332 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.335 2.440 ... (remaining 233764 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 17 through 42 or resid 44 through 401 or resid 403 through \ 1144 or resid 1301 through 1306)) selection = (chain 'B' and (resid 17 through 42 or resid 44 through 401 or resid 403 through \ 1144 or resid 1301 through 1306)) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 6.780 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: 23.640 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 76.370 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.300 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31161 Z= 0.248 Angle : 0.780 21.374 42386 Z= 0.458 Chirality : 0.051 0.591 4879 Planarity : 0.006 0.075 5421 Dihedral : 14.248 85.564 10987 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 0.45 % Allowed : 5.85 % Favored : 93.70 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.11), residues: 3726 helix: -3.14 (0.12), residues: 842 sheet: -1.81 (0.18), residues: 667 loop : -2.93 (0.10), residues: 2217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 808 time to evaluate : 3.796 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 outliers start: 15 outliers final: 3 residues processed: 816 average time/residue: 1.2040 time to fit residues: 1184.5955 Evaluate side-chains 665 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 662 time to evaluate : 3.263 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 4.5737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 0.0040 chunk 294 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 341 optimal weight: 8.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 132 GLN A 191 ASN A 311 GLN A 318 GLN A 357 ASN A 391 ASN A 447 ASN A 474 ASN A 478 ASN A 560 GLN A 610 GLN A 771 GLN A 910 GLN A 952 ASN A 962 GLN A 975 ASN A1002 GLN A1033 GLN A1051 GLN A1139 GLN B 113 GLN B 215 GLN B 318 GLN B 340 ASN B 411 GLN B 419 ASN B 478 ASN B 537 ASN B 553 ASN B 610 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 GLN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 ASN B1033 GLN B1068 GLN B1103 GLN C 97 ASN C 123 ASN C 268 GLN C 340 ASN C 411 GLN C 447 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN C 577 GLN C 774 ASN C 821 ASN C 916 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN C 962 GLN C1020 ASN C1061 HIS ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 340 GLN D 437 ASN D 472 GLN D 505 HIS D 522 GLN D 524 GLN D 578 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 31161 Z= 0.313 Angle : 0.614 10.384 42386 Z= 0.316 Chirality : 0.046 0.196 4879 Planarity : 0.005 0.058 5421 Dihedral : 4.741 35.760 4051 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.71 % Allowed : 15.23 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 3726 helix: -1.69 (0.16), residues: 877 sheet: -1.02 (0.19), residues: 660 loop : -2.46 (0.11), residues: 2189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 720 time to evaluate : 3.144 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 outliers start: 123 outliers final: 52 residues processed: 777 average time/residue: 1.2870 time to fit residues: 1197.3016 Evaluate side-chains 715 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 663 time to evaluate : 3.157 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 29 residues processed: 26 average time/residue: 0.6534 time to fit residues: 27.9644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 342 optimal weight: 0.9990 chunk 369 optimal weight: 10.0000 chunk 304 optimal weight: 0.9990 chunk 339 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 274 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 191 ASN A 236 GLN A 268 GLN A 560 GLN A 672 GLN A 898 GLN A1002 GLN A1116 ASN B 318 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN B 923 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN B1002 GLN B1008 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 123 ASN C 268 GLN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN C 700 ASN C 916 ASN C 962 GLN C1132 ASN D 24 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31161 Z= 0.295 Angle : 0.595 9.636 42386 Z= 0.305 Chirality : 0.045 0.181 4879 Planarity : 0.004 0.053 5421 Dihedral : 4.729 36.655 4051 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.34 % Allowed : 17.71 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.12), residues: 3726 helix: -0.99 (0.17), residues: 887 sheet: -0.75 (0.19), residues: 673 loop : -2.19 (0.12), residues: 2166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 699 time to evaluate : 3.317 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 outliers start: 144 outliers final: 69 residues processed: 761 average time/residue: 1.3036 time to fit residues: 1177.0680 Evaluate side-chains 738 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 669 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 35 residues processed: 35 average time/residue: 0.6313 time to fit residues: 32.4120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 8.9990 chunk 257 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 343 optimal weight: 1.9990 chunk 363 optimal weight: 0.0980 chunk 179 optimal weight: 0.3980 chunk 325 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 191 ASN A 236 GLN A 268 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 672 GLN A 910 GLN A 999 GLN B 191 ASN B 759 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 123 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 ASN C 962 GLN C 999 GLN C1002 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31161 Z= 0.223 Angle : 0.576 12.394 42386 Z= 0.292 Chirality : 0.044 0.317 4879 Planarity : 0.004 0.060 5421 Dihedral : 4.655 40.605 4051 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.80 % Allowed : 19.94 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.13), residues: 3726 helix: -0.60 (0.18), residues: 880 sheet: -0.39 (0.19), residues: 644 loop : -2.05 (0.12), residues: 2202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 697 time to evaluate : 3.035 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 outliers start: 126 outliers final: 81 residues processed: 757 average time/residue: 1.3544 time to fit residues: 1219.6326 Evaluate side-chains 752 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 671 time to evaluate : 2.966 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 48 residues processed: 36 average time/residue: 0.6046 time to fit residues: 34.7142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 0.9980 chunk 206 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 310 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 268 GLN A 318 GLN A 411 GLN A 560 GLN A 672 GLN A 910 GLN B 759 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN B1002 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 236 GLN C 516 HIS C 700 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN D 24 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31161 Z= 0.344 Angle : 0.612 10.150 42386 Z= 0.312 Chirality : 0.046 0.304 4879 Planarity : 0.004 0.051 5421 Dihedral : 4.854 36.365 4051 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.31 % Allowed : 20.60 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 3726 helix: -0.54 (0.17), residues: 896 sheet: -0.43 (0.19), residues: 653 loop : -1.91 (0.12), residues: 2177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 691 time to evaluate : 3.503 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 outliers start: 143 outliers final: 85 residues processed: 768 average time/residue: 1.3683 time to fit residues: 1253.7328 Evaluate side-chains 758 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 673 time to evaluate : 3.371 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 51 residues processed: 35 average time/residue: 0.6745 time to fit residues: 37.9632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 8.9990 chunk 327 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 213 optimal weight: 0.1980 chunk 89 optimal weight: 0.1980 chunk 363 optimal weight: 8.9990 chunk 301 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 318 GLN A 502 HIS A 560 GLN A 655 ASN A 910 GLN A 999 GLN B 759 GLN B 781 GLN B1002 GLN C 113 GLN C 123 ASN C 604 GLN C 700 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN C1002 GLN D 24 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31161 Z= 0.229 Angle : 0.579 9.668 42386 Z= 0.294 Chirality : 0.044 0.216 4879 Planarity : 0.004 0.050 5421 Dihedral : 4.731 40.134 4051 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.83 % Allowed : 21.96 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3726 helix: -0.29 (0.18), residues: 889 sheet: -0.33 (0.19), residues: 658 loop : -1.80 (0.12), residues: 2179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 674 time to evaluate : 3.376 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 outliers start: 127 outliers final: 73 residues processed: 751 average time/residue: 1.3169 time to fit residues: 1179.7954 Evaluate side-chains 739 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 666 time to evaluate : 3.103 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 50 residues processed: 23 average time/residue: 0.6303 time to fit residues: 24.4185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 265 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 362 optimal weight: 0.0170 chunk 226 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 318 GLN A 560 GLN A 600 ASN A 655 ASN A 672 GLN A 910 GLN A 952 ASN A 999 GLN B 553 ASN B 781 GLN B 999 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN C 999 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS D 572 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31161 Z= 0.218 Angle : 0.575 9.526 42386 Z= 0.292 Chirality : 0.044 0.323 4879 Planarity : 0.004 0.049 5421 Dihedral : 4.661 35.378 4051 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.53 % Allowed : 22.56 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3726 helix: -0.16 (0.18), residues: 895 sheet: -0.26 (0.19), residues: 660 loop : -1.72 (0.12), residues: 2171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 670 time to evaluate : 3.352 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 outliers start: 117 outliers final: 82 residues processed: 732 average time/residue: 1.3479 time to fit residues: 1184.5611 Evaluate side-chains 744 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 662 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 49 residues processed: 33 average time/residue: 0.6212 time to fit residues: 33.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 216 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 chunk 246 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 655 ASN A 910 GLN A1116 ASN B 553 ASN B 781 GLN B 954 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 700 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31161 Z= 0.235 Angle : 0.588 10.394 42386 Z= 0.298 Chirality : 0.045 0.326 4879 Planarity : 0.004 0.049 5421 Dihedral : 4.665 33.348 4051 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.93 % Allowed : 23.47 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 3726 helix: -0.03 (0.18), residues: 884 sheet: -0.24 (0.19), residues: 654 loop : -1.69 (0.13), residues: 2188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 661 time to evaluate : 3.564 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 outliers start: 97 outliers final: 74 residues processed: 726 average time/residue: 1.3659 time to fit residues: 1190.9398 Evaluate side-chains 727 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 653 time to evaluate : 3.350 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 56 residues processed: 19 average time/residue: 0.6886 time to fit residues: 22.7364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 30.0000 chunk 347 optimal weight: 0.7980 chunk 316 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 147 optimal weight: 0.0470 chunk 265 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 chunk 319 optimal weight: 8.9990 chunk 336 optimal weight: 9.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 655 ASN A 910 GLN A 999 GLN A1116 ASN B 553 ASN B 954 GLN C 119 ASN C 700 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31161 Z= 0.266 Angle : 0.606 10.767 42386 Z= 0.308 Chirality : 0.046 0.306 4879 Planarity : 0.004 0.048 5421 Dihedral : 4.724 31.663 4051 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 2.96 % Allowed : 23.65 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 3726 helix: -0.09 (0.18), residues: 896 sheet: -0.24 (0.19), residues: 669 loop : -1.66 (0.13), residues: 2161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7452 Ramachandran restraints generated. 3726 Oldfield, 0 Emsley, 3726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 668 time to evaluate : 3.241 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 outliers start: 98 outliers final: 75 residues processed: 731 average time/residue: 1.3194 time to fit residues: 1152.3987 Evaluate side-chains 735 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 660 time to evaluate : 3.215 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 58 residues processed: 17 average time/residue: 0.7987 time to fit residues: 22.4110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.8239 > 50: distance: 19 - 38: 6.351 distance: 24 - 46: 11.831 distance: 31 - 38: 6.231 distance: 38 - 39: 3.756 distance: 39 - 40: 18.061 distance: 39 - 42: 6.178 distance: 40 - 41: 13.320 distance: 40 - 46: 27.234 distance: 42 - 43: 7.936 distance: 43 - 44: 16.569 distance: 43 - 45: 8.250 distance: 46 - 47: 19.853 distance: 47 - 48: 8.356 distance: 47 - 50: 21.254 distance: 48 - 49: 8.940 distance: 48 - 55: 11.903 distance: 50 - 51: 19.977 distance: 51 - 52: 23.381 distance: 52 - 53: 12.868 distance: 53 - 54: 14.484 distance: 55 - 56: 11.116 distance: 56 - 57: 14.025 distance: 56 - 59: 10.994 distance: 57 - 58: 16.739 distance: 57 - 61: 11.139 distance: 59 - 60: 18.816 distance: 61 - 62: 30.851 distance: 62 - 63: 7.582 distance: 62 - 65: 11.428 distance: 63 - 64: 24.620 distance: 63 - 69: 17.188 distance: 65 - 66: 23.855 distance: 65 - 67: 3.242 distance: 66 - 68: 10.169 distance: 69 - 70: 34.667 distance: 70 - 71: 6.856 distance: 71 - 72: 10.590 distance: 71 - 73: 11.241 distance: 73 - 74: 12.223 distance: 74 - 75: 18.004 distance: 74 - 77: 9.628 distance: 75 - 76: 33.895 distance: 75 - 81: 9.326 distance: 77 - 78: 23.348 distance: 78 - 79: 21.050 distance: 78 - 80: 15.906 distance: 81 - 82: 11.093 distance: 82 - 83: 15.151 distance: 82 - 85: 11.050 distance: 83 - 84: 3.376 distance: 83 - 89: 28.147 distance: 85 - 86: 11.710 distance: 86 - 87: 30.788 distance: 86 - 88: 36.972 distance: 89 - 90: 22.796 distance: 90 - 91: 21.729 distance: 90 - 93: 12.970 distance: 91 - 92: 16.344 distance: 91 - 95: 13.218 distance: 93 - 94: 16.895 distance: 95 - 96: 22.642 distance: 95 - 101: 18.320 distance: 96 - 97: 20.287 distance: 96 - 99: 24.218 distance: 97 - 102: 40.115 distance: 99 - 100: 20.403 distance: 100 - 101: 11.308 distance: 102 - 103: 15.502 distance: 103 - 104: 15.437 distance: 103 - 106: 11.695 distance: 104 - 105: 20.292 distance: 104 - 110: 7.196 distance: 106 - 107: 9.499 distance: 107 - 108: 7.855 distance: 107 - 109: 11.825