Starting phenix.real_space_refine on Wed Feb 21 18:34:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkv_24504/02_2024/7rkv_24504.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkv_24504/02_2024/7rkv_24504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkv_24504/02_2024/7rkv_24504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkv_24504/02_2024/7rkv_24504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkv_24504/02_2024/7rkv_24504.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkv_24504/02_2024/7rkv_24504.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 19952 2.51 5 N 5287 2.21 5 O 5983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "H TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 65": "NH1" <-> "NH2" Residue "H TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 143": "OD1" <-> "OD2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "F TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 143": "OD1" <-> "OD2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 222": "OD1" <-> "OD2" Residue "L TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 143": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31357 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 8, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 437 Chain: "B" Number of atoms: 7026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7026 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 788 Unresolved non-hydrogen angles: 1010 Unresolved non-hydrogen dihedrals: 620 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 10, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 460 Chain: "C" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 8, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 437 Chain: "D" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1590 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1590 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1590 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.42, per 1000 atoms: 0.52 Number of scatterers: 31357 At special positions: 0 Unit cell: (133.826, 145.992, 212.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5983 8.00 N 5287 7.00 C 19952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 210 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 198 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 198 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 331 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG A1314 " - " ASN A 717 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG B1314 " - " ASN B 717 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 717 " Time building additional restraints: 11.90 Conformation dependent library (CDL) restraints added in 6.1 seconds 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7950 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 84 sheets defined 21.3% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.055A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.370A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.686A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.098A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.763A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.660A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 342' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.055A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.153A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.687A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.099A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 967 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.763A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.764A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.055A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.687A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.099A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.762A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.704A pdb=" N LEU D 203 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 126 through 131 Processing helix chain 'H' and resid 186 through 192 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 199 through 205 removed outlier: 3.705A pdb=" N LEU E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY E 204 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 126 through 131 Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 170 through 172 No H-bonds generated for 'chain 'G' and resid 170 through 172' Processing helix chain 'G' and resid 199 through 205 removed outlier: 3.704A pdb=" N LEU G 203 " --> pdb=" O SER G 200 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY G 204 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 218 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 186 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.252A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.533A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.531A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.156A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.989A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.233A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.378A pdb=" N PHE A 377 " --> pdb=" O TYR E 103 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR E 103 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.957A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.864A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 719 through 728 removed outlier: 7.027A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.365A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1103 through 1104 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.681A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.531A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.156A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.990A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.234A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.335A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.828A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.864A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.027A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.364A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.681A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.531A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 11.212A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.989A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.602A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.284A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.864A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.028A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.502A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.364A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.265A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.614A pdb=" N GLY D 109 " --> pdb=" O ASP D 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 134 through 136 removed outlier: 5.288A pdb=" N GLY D 153 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL D 196 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU D 155 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER D 194 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS D 157 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU D 192 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 134 through 136 removed outlier: 5.288A pdb=" N GLY D 153 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL D 196 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU D 155 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER D 194 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS D 157 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU D 192 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 165 through 168 removed outlier: 4.567A pdb=" N TYR D 208 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.543A pdb=" N ALA H 12 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE H 33 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS H 49 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.543A pdb=" N ALA H 12 " --> pdb=" O THR H 109 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 119 through 123 removed outlier: 5.216A pdb=" N THR H 136 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU H 185 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL H 138 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU H 183 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU H 140 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER H 181 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER H 142 " --> pdb=" O ALA H 179 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA H 179 " --> pdb=" O SER H 142 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 119 through 123 removed outlier: 5.216A pdb=" N THR H 136 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU H 185 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL H 138 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU H 183 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU H 140 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER H 181 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER H 142 " --> pdb=" O ALA H 179 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA H 179 " --> pdb=" O SER H 142 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 158 through 160 removed outlier: 4.658A pdb=" N TRP H 153 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.874A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.587A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG9, first strand: chain 'E' and resid 134 through 136 removed outlier: 5.287A pdb=" N GLY E 153 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL E 196 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 155 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER E 194 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 157 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU E 192 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 134 through 136 removed outlier: 5.287A pdb=" N GLY E 153 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL E 196 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 155 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER E 194 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 157 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU E 192 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 165 through 168 removed outlier: 4.567A pdb=" N TYR E 208 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AH4, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.566A pdb=" N ALA F 12 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE F 33 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.566A pdb=" N ALA F 12 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.218A pdb=" N THR F 136 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU F 185 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL F 138 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU F 183 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU F 140 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER F 181 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER F 142 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA F 179 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.218A pdb=" N THR F 136 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU F 185 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL F 138 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU F 183 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU F 140 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER F 181 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER F 142 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA F 179 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 158 through 160 removed outlier: 4.661A pdb=" N TRP F 153 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.874A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.600A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AI3, first strand: chain 'G' and resid 101 through 104 removed outlier: 3.565A pdb=" N GLY G 109 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 134 through 136 removed outlier: 5.287A pdb=" N GLY G 153 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL G 196 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU G 155 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER G 194 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS G 157 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU G 192 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 134 through 136 removed outlier: 5.287A pdb=" N GLY G 153 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL G 196 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU G 155 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER G 194 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS G 157 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU G 192 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 165 through 168 removed outlier: 4.567A pdb=" N TYR G 208 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AI8, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.550A pdb=" N ALA L 12 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.550A pdb=" N ALA L 12 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.217A pdb=" N THR L 136 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU L 185 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL L 138 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU L 183 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU L 140 " --> pdb=" O SER L 181 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER L 181 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER L 142 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA L 179 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.217A pdb=" N THR L 136 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU L 185 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL L 138 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU L 183 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU L 140 " --> pdb=" O SER L 181 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER L 181 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER L 142 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA L 179 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 158 through 160 removed outlier: 4.659A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) 1498 hydrogen bonds defined for protein. 3834 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: 17.62 Time building geometry restraints manager: 12.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5115 1.31 - 1.44: 8794 1.44 - 1.57: 17985 1.57 - 1.70: 6 1.70 - 1.84: 168 Bond restraints: 32068 Sorted by residual: bond pdb=" CB ASN B 928 " pdb=" CG ASN B 928 " ideal model delta sigma weight residual 1.516 1.297 0.219 2.50e-02 1.60e+03 7.65e+01 bond pdb=" CB ASN C 928 " pdb=" CG ASN C 928 " ideal model delta sigma weight residual 1.516 1.298 0.218 2.50e-02 1.60e+03 7.61e+01 bond pdb=" CB ASN A 928 " pdb=" CG ASN A 928 " ideal model delta sigma weight residual 1.516 1.298 0.218 2.50e-02 1.60e+03 7.59e+01 bond pdb=" C PHE A1075 " pdb=" N THR A1076 " ideal model delta sigma weight residual 1.330 1.456 -0.126 1.45e-02 4.76e+03 7.58e+01 bond pdb=" C PHE C1075 " pdb=" N THR C1076 " ideal model delta sigma weight residual 1.330 1.456 -0.126 1.45e-02 4.76e+03 7.55e+01 ... (remaining 32063 not shown) Histogram of bond angle deviations from ideal: 96.63 - 105.76: 998 105.76 - 114.90: 18932 114.90 - 124.03: 22557 124.03 - 133.17: 1315 133.17 - 142.30: 49 Bond angle restraints: 43851 Sorted by residual: angle pdb=" C PHE A1075 " pdb=" N THR A1076 " pdb=" CA THR A1076 " ideal model delta sigma weight residual 122.09 96.63 25.46 1.48e+00 4.57e-01 2.96e+02 angle pdb=" C PHE B1075 " pdb=" N THR B1076 " pdb=" CA THR B1076 " ideal model delta sigma weight residual 122.09 96.64 25.45 1.48e+00 4.57e-01 2.96e+02 angle pdb=" C PHE C1075 " pdb=" N THR C1076 " pdb=" CA THR C1076 " ideal model delta sigma weight residual 122.09 96.64 25.45 1.48e+00 4.57e-01 2.96e+02 angle pdb=" CA GLN A 926 " pdb=" CB GLN A 926 " pdb=" CG GLN A 926 " ideal model delta sigma weight residual 114.10 142.30 -28.20 2.00e+00 2.50e-01 1.99e+02 angle pdb=" CA GLN B 926 " pdb=" CB GLN B 926 " pdb=" CG GLN B 926 " ideal model delta sigma weight residual 114.10 142.28 -28.18 2.00e+00 2.50e-01 1.99e+02 ... (remaining 43846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 18378 18.00 - 36.00: 832 36.00 - 54.00: 186 54.00 - 72.00: 50 72.00 - 89.99: 22 Dihedral angle restraints: 19468 sinusoidal: 7097 harmonic: 12371 Sorted by residual: dihedral pdb=" C ASN A1134 " pdb=" N ASN A1134 " pdb=" CA ASN A1134 " pdb=" CB ASN A1134 " ideal model delta harmonic sigma weight residual -122.60 -156.11 33.51 0 2.50e+00 1.60e-01 1.80e+02 dihedral pdb=" N ASN A1134 " pdb=" C ASN A1134 " pdb=" CA ASN A1134 " pdb=" CB ASN A1134 " ideal model delta harmonic sigma weight residual 122.80 155.56 -32.76 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.42e+01 ... (remaining 19465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.272: 5159 0.272 - 0.544: 31 0.544 - 0.815: 0 0.815 - 1.087: 0 1.087 - 1.359: 1 Chirality restraints: 5191 Sorted by residual: chirality pdb=" CA ASN A1134 " pdb=" N ASN A1134 " pdb=" C ASN A1134 " pdb=" CB ASN A1134 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.62e+01 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PHE B 342 " pdb=" N PHE B 342 " pdb=" C PHE B 342 " pdb=" CB PHE B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5188 not shown) Planarity restraints: 5699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.352 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C1303 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " 0.327 2.00e-02 2.50e+03 2.78e-01 9.63e+02 pdb=" C7 NAG C1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1312 " -0.273 2.00e-02 2.50e+03 2.31e-01 6.69e+02 pdb=" C7 NAG A1312 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1312 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A1312 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG A1312 " -0.017 2.00e-02 2.50e+03 ... (remaining 5696 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 90 2.44 - 3.06: 20054 3.06 - 3.67: 44883 3.67 - 4.29: 68483 4.29 - 4.90: 113438 Nonbonded interactions: 246948 Sorted by model distance: nonbonded pdb=" CG PRO B 412 " pdb=" OH TYR D 32 " model vdw 1.829 3.440 nonbonded pdb=" CD1 TRP L 95 " pdb=" CD2 LEU L 100 " model vdw 1.905 3.680 nonbonded pdb=" CG PRO C 412 " pdb=" OH TYR G 32 " model vdw 1.916 3.440 nonbonded pdb=" ND2 ASN B 801 " pdb=" O7 NAG B1311 " model vdw 2.038 2.520 nonbonded pdb=" CG1 VAL D 64 " pdb=" CB PHE D 68 " model vdw 2.083 3.860 ... (remaining 246943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1145 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 510 or (resid 511 through 512 and (name N or na \ me CA or name C or name O or name CB )) or resid 513 through 1145 or resid 1301 \ through 1311)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1145 or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.590 Check model and map are aligned: 0.580 Set scattering table: 0.290 Process input model: 88.320 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 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 : 0.009 0.219 32068 Z= 0.575 Angle : 1.343 28.205 43851 Z= 0.841 Chirality : 0.076 1.359 5191 Planarity : 0.012 0.301 5660 Dihedral : 11.812 89.994 11365 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 0.54 % Allowed : 4.88 % Favored : 94.58 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 4212 helix: 1.05 (0.19), residues: 705 sheet: 0.35 (0.15), residues: 1200 loop : -0.39 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.005 TRP B1102 HIS 0.012 0.002 HIS C1083 PHE 0.093 0.003 PHE C 374 TYR 0.045 0.003 TYR C 170 ARG 0.017 0.002 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 234 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 THR cc_start: 0.9386 (p) cc_final: 0.8876 (t) REVERT: C 883 THR cc_start: 0.9493 (p) cc_final: 0.9231 (t) REVERT: E 168 TRP cc_start: 0.0880 (m100) cc_final: 0.0577 (m100) REVERT: G 168 TRP cc_start: 0.0896 (m100) cc_final: 0.0518 (m100) outliers start: 16 outliers final: 3 residues processed: 250 average time/residue: 0.4710 time to fit residues: 186.4044 Evaluate side-chains 114 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 4.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 75 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 357 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 109 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 331 optimal weight: 30.0000 chunk 128 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 246 optimal weight: 7.9990 chunk 384 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN A1071 GLN A1113 GLN B1005 GLN B1071 GLN B1113 GLN C1071 GLN C1113 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32068 Z= 0.232 Angle : 0.624 8.849 43851 Z= 0.327 Chirality : 0.046 0.405 5191 Planarity : 0.005 0.096 5660 Dihedral : 6.158 57.591 5352 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.61 % Favored : 98.36 % Rotamer: Outliers : 1.49 % Allowed : 6.98 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.12), residues: 4212 helix: 1.71 (0.18), residues: 732 sheet: 0.49 (0.14), residues: 1299 loop : -0.07 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 168 HIS 0.005 0.001 HIS C 655 PHE 0.026 0.002 PHE C1075 TYR 0.023 0.002 TYR H 177 ARG 0.013 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 4.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 155 LEU cc_start: 0.0744 (OUTLIER) cc_final: 0.0320 (mm) REVERT: E 168 TRP cc_start: 0.1248 (m100) cc_final: 0.0467 (m100) outliers start: 44 outliers final: 19 residues processed: 169 average time/residue: 0.4700 time to fit residues: 127.9698 Evaluate side-chains 135 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 75 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 213 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 chunk 261 optimal weight: 0.3980 chunk 105 optimal weight: 8.9990 chunk 384 optimal weight: 10.0000 chunk 415 optimal weight: 10.0000 chunk 342 optimal weight: 8.9990 chunk 381 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 308 optimal weight: 20.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 207 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN H 38 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 32068 Z= 0.408 Angle : 0.671 9.189 43851 Z= 0.349 Chirality : 0.046 0.321 5191 Planarity : 0.005 0.046 5660 Dihedral : 5.616 53.051 5352 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 1.83 % Allowed : 8.47 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 4212 helix: 2.30 (0.19), residues: 687 sheet: 0.65 (0.14), residues: 1215 loop : -0.02 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 168 HIS 0.010 0.002 HIS A 655 PHE 0.021 0.002 PHE C1103 TYR 0.033 0.002 TYR B 904 ARG 0.009 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 111 time to evaluate : 3.883 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: D 155 LEU cc_start: 0.0539 (OUTLIER) cc_final: 0.0323 (mm) REVERT: E 168 TRP cc_start: 0.1610 (m100) cc_final: 0.0859 (m100) REVERT: G 83 MET cc_start: 0.1409 (mtt) cc_final: 0.1195 (mpp) REVERT: G 168 TRP cc_start: 0.1588 (m100) cc_final: 0.1380 (m100) outliers start: 54 outliers final: 35 residues processed: 152 average time/residue: 0.4515 time to fit residues: 112.0996 Evaluate side-chains 118 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 82 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 75 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 380 optimal weight: 10.0000 chunk 289 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 386 optimal weight: 0.3980 chunk 408 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 366 optimal weight: 0.7980 chunk 110 optimal weight: 30.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 901 GLN B1135 ASN C 901 GLN C1135 ASN H 28 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 37 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32068 Z= 0.156 Angle : 0.499 6.073 43851 Z= 0.262 Chirality : 0.044 0.366 5191 Planarity : 0.004 0.045 5660 Dihedral : 5.086 59.123 5351 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.90 % Favored : 98.08 % Rotamer: Outliers : 1.15 % Allowed : 9.83 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.13), residues: 4212 helix: 2.60 (0.20), residues: 684 sheet: 0.74 (0.14), residues: 1227 loop : 0.05 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.004 0.001 HIS G 35 PHE 0.015 0.001 PHE C1103 TYR 0.017 0.001 TYR B 904 ARG 0.003 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 3.702 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: A 1029 MET cc_start: 0.9155 (tpp) cc_final: 0.8772 (ttm) REVERT: B 740 MET cc_start: 0.9043 (tpt) cc_final: 0.8813 (tpp) REVERT: C 697 MET cc_start: 0.8792 (ttm) cc_final: 0.8517 (ttp) REVERT: E 168 TRP cc_start: 0.1491 (m100) cc_final: 0.1263 (m100) REVERT: G 83 MET cc_start: 0.1605 (mtt) cc_final: 0.1335 (mpp) REVERT: G 168 TRP cc_start: 0.1503 (m100) cc_final: 0.1191 (m100) REVERT: L 65 ARG cc_start: 0.3750 (ptt180) cc_final: 0.3462 (ptt90) outliers start: 34 outliers final: 18 residues processed: 135 average time/residue: 0.4488 time to fit residues: 99.5534 Evaluate side-chains 110 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 115 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 340 optimal weight: 5.9990 chunk 232 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 304 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 348 optimal weight: 30.0000 chunk 282 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 366 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS B1088 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 57 ASN E 185 GLN F 28 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 57 ASN G 185 GLN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 32068 Z= 0.412 Angle : 0.661 9.827 43851 Z= 0.338 Chirality : 0.045 0.393 5191 Planarity : 0.005 0.045 5660 Dihedral : 5.483 59.343 5351 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 2.10 % Allowed : 10.03 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4212 helix: 2.27 (0.20), residues: 687 sheet: 0.61 (0.14), residues: 1233 loop : -0.05 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.008 0.002 HIS B 655 PHE 0.021 0.002 PHE H 144 TYR 0.026 0.002 TYR B 904 ARG 0.005 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 91 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9351 (tpp) cc_final: 0.8794 (ttm) REVERT: B 740 MET cc_start: 0.9092 (tpt) cc_final: 0.8841 (tpp) REVERT: C 740 MET cc_start: 0.9218 (tpp) cc_final: 0.8997 (tpp) REVERT: E 168 TRP cc_start: 0.1776 (m100) cc_final: 0.1574 (m100) REVERT: G 83 MET cc_start: 0.1916 (mtt) cc_final: 0.1649 (mtt) REVERT: G 168 TRP cc_start: 0.1910 (m100) cc_final: 0.1589 (m100) outliers start: 62 outliers final: 37 residues processed: 143 average time/residue: 0.4395 time to fit residues: 103.0050 Evaluate side-chains 118 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 81 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 115 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 137 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 409 optimal weight: 20.0000 chunk 339 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 135 optimal weight: 0.0030 chunk 214 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN F 28 HIS F 37 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32068 Z= 0.169 Angle : 0.502 7.349 43851 Z= 0.260 Chirality : 0.044 0.293 5191 Planarity : 0.004 0.099 5660 Dihedral : 4.778 57.605 5347 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.39 % Allowed : 10.88 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4212 helix: 2.70 (0.20), residues: 684 sheet: 0.73 (0.15), residues: 1194 loop : 0.05 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.005 0.001 HIS H 56 PHE 0.019 0.001 PHE H 144 TYR 0.014 0.001 TYR D 94 ARG 0.014 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 97 time to evaluate : 3.788 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: A 1029 MET cc_start: 0.9172 (tpp) cc_final: 0.8713 (ttm) REVERT: B 740 MET cc_start: 0.9025 (tpt) cc_final: 0.8809 (tpp) REVERT: C 242 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 697 MET cc_start: 0.8752 (ttm) cc_final: 0.8451 (ttp) REVERT: C 740 MET cc_start: 0.9146 (tpp) cc_final: 0.8913 (tpp) REVERT: C 1111 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7981 (pp20) REVERT: H 65 ARG cc_start: 0.2858 (ptt90) cc_final: 0.1782 (ptm-80) REVERT: F 65 ARG cc_start: 0.2735 (ptm-80) cc_final: 0.2346 (ptt90) REVERT: G 83 MET cc_start: 0.2085 (mtt) cc_final: 0.1817 (mtt) REVERT: G 168 TRP cc_start: 0.1826 (m100) cc_final: 0.1558 (m100) outliers start: 41 outliers final: 22 residues processed: 134 average time/residue: 0.4362 time to fit residues: 97.5244 Evaluate side-chains 113 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 394 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 298 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 344 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 407 optimal weight: 0.0670 chunk 255 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32068 Z= 0.186 Angle : 0.501 9.344 43851 Z= 0.257 Chirality : 0.044 0.458 5191 Planarity : 0.004 0.064 5660 Dihedral : 4.423 50.812 5347 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.42 % Allowed : 11.12 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.13), residues: 4212 helix: 2.59 (0.20), residues: 702 sheet: 0.81 (0.15), residues: 1182 loop : 0.12 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 168 HIS 0.005 0.001 HIS H 56 PHE 0.021 0.001 PHE H 144 TYR 0.015 0.001 TYR C 873 ARG 0.008 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 96 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 740 MET cc_start: 0.9155 (tpp) cc_final: 0.8755 (tpp) REVERT: A 1029 MET cc_start: 0.9174 (tpp) cc_final: 0.8725 (ttm) REVERT: B 242 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8460 (tt) REVERT: B 740 MET cc_start: 0.9031 (tpt) cc_final: 0.8814 (tpp) REVERT: C 242 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8644 (tt) REVERT: C 697 MET cc_start: 0.8700 (ttm) cc_final: 0.8398 (ttp) REVERT: C 740 MET cc_start: 0.9130 (tpp) cc_final: 0.8867 (tpp) REVERT: C 1111 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7932 (pp20) REVERT: G 83 MET cc_start: 0.1939 (mtt) cc_final: 0.1716 (mtt) outliers start: 42 outliers final: 25 residues processed: 135 average time/residue: 0.4136 time to fit residues: 94.0776 Evaluate side-chains 117 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 252 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 259 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 37 optimal weight: 0.0980 chunk 320 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN C 121 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN F 28 HIS F 38 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5674 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32068 Z= 0.131 Angle : 0.481 9.574 43851 Z= 0.245 Chirality : 0.044 0.440 5191 Planarity : 0.004 0.044 5660 Dihedral : 4.124 53.068 5347 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.15 % Allowed : 11.39 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.13), residues: 4212 helix: 2.78 (0.20), residues: 687 sheet: 0.84 (0.15), residues: 1218 loop : 0.16 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E 168 HIS 0.004 0.001 HIS G 35 PHE 0.017 0.001 PHE H 144 TYR 0.024 0.001 TYR H 177 ARG 0.007 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 740 MET cc_start: 0.9175 (tpp) cc_final: 0.8720 (tpp) REVERT: A 1029 MET cc_start: 0.9119 (tpp) cc_final: 0.8725 (ttm) REVERT: B 242 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8511 (tt) REVERT: B 740 MET cc_start: 0.9014 (tpt) cc_final: 0.8803 (tpp) REVERT: C 242 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8647 (tt) REVERT: C 697 MET cc_start: 0.8713 (ttm) cc_final: 0.8313 (ttp) REVERT: C 740 MET cc_start: 0.9106 (tpp) cc_final: 0.8848 (tpp) REVERT: C 1111 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7891 (pp20) REVERT: E 34 MET cc_start: 0.6044 (tpp) cc_final: 0.5557 (mmm) outliers start: 34 outliers final: 21 residues processed: 128 average time/residue: 0.4278 time to fit residues: 93.4821 Evaluate side-chains 115 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 370 optimal weight: 6.9990 chunk 390 optimal weight: 50.0000 chunk 356 optimal weight: 20.0000 chunk 379 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 298 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 378 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS B 655 HIS B1135 ASN C 81 ASN C 655 HIS ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 77 ASN L 38 GLN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 32068 Z= 0.487 Angle : 0.671 9.324 43851 Z= 0.337 Chirality : 0.046 0.461 5191 Planarity : 0.005 0.072 5660 Dihedral : 4.849 49.352 5347 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.49 % Allowed : 11.36 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 4212 helix: 2.31 (0.20), residues: 705 sheet: 0.69 (0.15), residues: 1233 loop : 0.00 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 168 HIS 0.008 0.002 HIS A1083 PHE 0.018 0.002 PHE H 66 TYR 0.018 0.002 TYR H 177 ARG 0.019 0.001 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 82 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8637 (tt) REVERT: A 1029 MET cc_start: 0.9371 (tpp) cc_final: 0.8839 (ttm) REVERT: B 242 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (tt) REVERT: B 740 MET cc_start: 0.9103 (tpt) cc_final: 0.8837 (tpp) REVERT: C 740 MET cc_start: 0.9192 (tpp) cc_final: 0.8882 (tpp) REVERT: C 1111 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8044 (pp20) REVERT: E 34 MET cc_start: 0.6159 (tpp) cc_final: 0.5824 (mmm) outliers start: 44 outliers final: 31 residues processed: 121 average time/residue: 0.4447 time to fit residues: 91.0764 Evaluate side-chains 112 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 78 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 249 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 279 optimal weight: 0.9990 chunk 421 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 335 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 259 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 51 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32068 Z= 0.244 Angle : 0.544 11.948 43851 Z= 0.276 Chirality : 0.044 0.428 5191 Planarity : 0.004 0.043 5660 Dihedral : 4.576 51.812 5347 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.02 % Allowed : 11.93 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.13), residues: 4212 helix: 2.53 (0.20), residues: 705 sheet: 0.66 (0.15), residues: 1224 loop : 0.03 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 168 HIS 0.006 0.001 HIS H 56 PHE 0.021 0.001 PHE H 144 TYR 0.017 0.001 TYR H 177 ARG 0.007 0.000 ARG L 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 740 MET cc_start: 0.9224 (tpp) cc_final: 0.8726 (tpp) REVERT: A 1029 MET cc_start: 0.9248 (tpp) cc_final: 0.8740 (ttm) REVERT: B 242 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8467 (tt) REVERT: B 740 MET cc_start: 0.9076 (tpt) cc_final: 0.8812 (tpp) REVERT: C 740 MET cc_start: 0.9153 (tpp) cc_final: 0.8847 (tpp) REVERT: C 1111 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8002 (pp20) REVERT: E 34 MET cc_start: 0.6152 (tpp) cc_final: 0.5799 (mmm) outliers start: 30 outliers final: 23 residues processed: 113 average time/residue: 0.4557 time to fit residues: 86.4543 Evaluate side-chains 104 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 266 optimal weight: 0.9990 chunk 357 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 309 optimal weight: 50.0000 chunk 49 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 336 optimal weight: 30.0000 chunk 140 optimal weight: 20.0000 chunk 345 optimal weight: 0.2980 chunk 42 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN L 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.095622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062405 restraints weight = 147782.545| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.65 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32068 Z= 0.221 Angle : 0.521 11.342 43851 Z= 0.263 Chirality : 0.044 0.403 5191 Planarity : 0.004 0.043 5660 Dihedral : 4.310 51.747 5347 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.15 % Allowed : 11.59 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.13), residues: 4212 helix: 2.70 (0.20), residues: 702 sheet: 0.67 (0.15), residues: 1230 loop : 0.06 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 168 HIS 0.005 0.001 HIS H 56 PHE 0.018 0.001 PHE H 144 TYR 0.017 0.001 TYR H 177 ARG 0.009 0.000 ARG C1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5094.65 seconds wall clock time: 95 minutes 12.53 seconds (5712.53 seconds total)