Starting phenix.real_space_refine on Sun Feb 18 20:43:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsb_21375/02_2024/6vsb_21375.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsb_21375/02_2024/6vsb_21375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsb_21375/02_2024/6vsb_21375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsb_21375/02_2024/6vsb_21375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsb_21375/02_2024/6vsb_21375.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsb_21375/02_2024/6vsb_21375.pdb" } resolution = 3.46 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 14551 2.51 5 N 3712 2.21 5 O 4490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22854 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7311 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 46, 'TRANS': 912} Chain breaks: 13 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7362 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 48, 'TRANS': 924} Chain breaks: 13 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 175 Chain: "C" Number of atoms: 7327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7327 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 209 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 11.58, per 1000 atoms: 0.51 Number of scatterers: 22854 At special positions: 0 Unit cell: (132.969, 131.922, 182.178, 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 101 16.00 O 4490 8.00 N 3712 7.00 C 14551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1315 " - " ASN A 122 " " NAG A1316 " - " ASN A 165 " " NAG A1317 " - " ASN A 234 " " NAG A1318 " - " ASN A 282 " " NAG A1319 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1315 " - " ASN B 343 " " NAG B1316 " - " ASN B 282 " " NAG B1317 " - " ASN B 234 " " NAG B1318 " - " ASN B 165 " " NAG B1319 " - " ASN B 122 " " NAG C1313 " - " ASN C 657 " " NAG C1314 " - " ASN C 616 " " NAG C1315 " - " ASN C 603 " " NAG C1316 " - " ASN C 122 " " NAG C1317 " - " ASN C 165 " " NAG C1318 " - " ASN C 234 " " NAG C1319 " - " ASN C 282 " " NAG C1320 " - " ASN C 331 " " NAG C1321 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 709 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1074 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 709 " Time building additional restraints: 9.35 Conformation dependent library (CDL) restraints added in 3.9 seconds 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5466 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 42 sheets defined 26.4% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.650A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.613A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.637A 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 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.679A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.656A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.776A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.533A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.510A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.830A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.637A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.950A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.680A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.516A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.600A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.061A 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 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.876A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.605A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 884 removed outlier: 4.439A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.982A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.844A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.610A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.907A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.625A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1120 Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.527A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 5.280A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.810A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.691A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.554A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.525A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.593A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.655A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.336A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.925A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.734A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.840A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.415A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.627A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.557A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.288A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.361A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.120A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.120A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.112A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.901A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.672A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.599A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AB9, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.122A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.327A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.501A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.725A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 451 through 453 removed outlier: 4.321A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.404A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.443A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.443A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TRP B1102 " --> pdb=" O GLN B1113 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN B1113 " --> pdb=" O TRP B1102 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B1104 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU B1111 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B1106 " --> pdb=" O PHE B1109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.223A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1122 through 1125 removed outlier: 5.423A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.726A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.036A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 224 through 227 removed outlier: 6.760A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.597A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.530A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.506A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE C 515 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.878A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 451 through 453 removed outlier: 4.070A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.383A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.040A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.040A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.184A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.785A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2472 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: 10.69 Time building geometry restraints manager: 10.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7231 1.35 - 1.48: 6170 1.48 - 1.61: 9796 1.61 - 1.75: 5 1.75 - 1.88: 120 Bond restraints: 23322 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" CA ASN A 709 " pdb=" C ASN A 709 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.41e-02 5.03e+03 8.69e+00 bond pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.76e+00 bond pdb=" C1 NAG A1316 " pdb=" O5 NAG A1316 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " ideal model delta sigma weight residual 1.808 1.721 0.087 3.30e-02 9.18e+02 6.97e+00 ... (remaining 23317 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.43: 390 104.43 - 111.82: 11307 111.82 - 119.21: 7606 119.21 - 126.60: 12254 126.60 - 133.99: 232 Bond angle restraints: 31789 Sorted by residual: angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 122.38 111.45 10.93 1.81e+00 3.05e-01 3.65e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 127.47 -13.07 2.30e+00 1.89e-01 3.23e+01 angle pdb=" CB MET C 697 " pdb=" CG MET C 697 " pdb=" SD MET C 697 " ideal model delta sigma weight residual 112.70 97.03 15.67 3.00e+00 1.11e-01 2.73e+01 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 112.96 107.77 5.19 1.00e+00 1.00e+00 2.70e+01 angle pdb=" C ASN B 542 " pdb=" N PHE B 543 " pdb=" CA PHE B 543 " ideal model delta sigma weight residual 121.54 131.17 -9.63 1.91e+00 2.74e-01 2.54e+01 ... (remaining 31784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13567 17.99 - 35.97: 802 35.97 - 53.96: 186 53.96 - 71.95: 44 71.95 - 89.94: 21 Dihedral angle restraints: 14620 sinusoidal: 6176 harmonic: 8444 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -172.86 86.86 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 10.32 82.68 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -15.39 -70.61 1 1.00e+01 1.00e-02 6.41e+01 ... (remaining 14617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 3867 0.253 - 0.506: 16 0.506 - 0.759: 5 0.759 - 1.012: 0 1.012 - 1.265: 1 Chirality restraints: 3889 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-02 2.50e+03 4.00e+03 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-02 2.50e+03 1.31e+03 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-02 2.50e+03 6.98e+02 ... (remaining 3886 not shown) Planarity restraints: 4064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " 0.359 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG P 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " -0.547 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.346 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG N 2 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.339 2.00e-02 2.50e+03 2.91e-01 1.05e+03 pdb=" C7 NAG I 1 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.513 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.094 2.00e-02 2.50e+03 ... (remaining 4061 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 340 2.62 - 3.19: 21225 3.19 - 3.76: 33627 3.76 - 4.33: 46869 4.33 - 4.90: 76492 Nonbonded interactions: 178553 Sorted by model distance: nonbonded pdb=" O3 NAG I 2 " pdb=" O7 NAG I 2 " model vdw 2.054 2.440 nonbonded pdb=" OG SER B 708 " pdb=" OD1 ASN B 710 " model vdw 2.093 2.440 nonbonded pdb=" OG SER A 708 " pdb=" OD1 ASN A 710 " model vdw 2.093 2.440 nonbonded pdb=" N GLU B1072 " pdb=" OE1 GLU B1072 " model vdw 2.100 2.520 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.109 2.440 ... (remaining 178548 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 95 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA or n \ ame C or name O or name CB )) or resid 130 through 140 or (resid 157 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or resid 217 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 243 or resid 264 through 344 or (resid 345 through 346 and (name N o \ r name CA or name C or name O or name CB )) or resid 347 through 350 or (resid 3 \ 51 through 352 and (name N or name CA or name C or name O or name CB )) or resid \ 353 through 363 or (resid 364 and (name N or name CA or name C or name O or nam \ e CB )) or resid 365 through 368 or (resid 369 and (name N or name CA or name C \ or name O or name CB )) or resid 370 through 373 or (resid 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 through 407 or (resid 408 a \ nd (name N or name CA or name C or name O or name CB )) or resid 409 through 441 \ or (resid 442 and (name N or name CA or name C or name O or name CB )) or resid \ 443 or (resid 449 and (name N or name CA or name C or name O or name CB )) or r \ esid 450 through 496 or (resid 497 through 498 and (name N or name CA or name C \ or name O or name CB )) or resid 503 through 504 or (resid 505 and (name N or na \ me CA or name C or name O or name CB )) or resid 506 through 508 or (resid 509 a \ nd (name N or name CA or name C or name O or name CB )) or resid 510 through 620 \ or resid 641 through 1146 or resid 1301 through 1319)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 or (resid 239 and (n \ ame N or name CA or name C or name O or name CB )) or resid 240 through 289 or ( \ resid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 328 or resid 335 through 350 or (resid 351 through 352 and (name N or na \ me CA or name C or name O or name CB )) or resid 353 through 363 or (resid 364 a \ nd (name N or name CA or name C or name O or name CB )) or resid 365 through 373 \ or (resid 374 and (name N or name CA or name C or name O or name CB )) or resid \ 375 through 441 or (resid 442 and (name N or name CA or name C or name O or nam \ e CB )) or resid 443 through 454 or resid 491 through 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 503 throug \ h 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) or \ resid 510 through 527 or (resid 528 through 529 and (name N or name CA or name C \ or name O or name CB )) or resid 530 through 620 or resid 641 through 1146 or r \ esid 1301 through 1319)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 66 or resid 81 throug \ h 95 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 104 or (resid 105 and (name N or name CA or name C o \ r name O or name CB )) or resid 106 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 209 \ or resid 217 through 243 or resid 264 through 328 or resid 335 through 344 or (r \ esid 345 through 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 454 or resid 491 through 504 or (resid 505 and (name N or nam \ e CA or name C or name O or name CB )) or resid 506 through 1146 or resid 1313 t \ hrough 1321)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.300 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: 0.000 Extract box with map and model: 17.870 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 63.940 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.280 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 23322 Z= 0.341 Angle : 0.919 15.666 31789 Z= 0.509 Chirality : 0.066 1.265 3889 Planarity : 0.015 0.309 4020 Dihedral : 12.569 89.935 9049 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.65 % Rotamer: Outliers : 0.59 % Allowed : 3.39 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 2821 helix: -0.34 (0.19), residues: 646 sheet: -0.73 (0.22), residues: 519 loop : -1.57 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1102 HIS 0.011 0.002 HIS B 655 PHE 0.033 0.002 PHE C 888 TYR 0.032 0.002 TYR B 660 ARG 0.012 0.001 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 2.615 Fit side-chains revert: symmetry clash REVERT: B 562 PHE cc_start: 0.7284 (p90) cc_final: 0.7017 (p90) REVERT: B 763 LEU cc_start: 0.9105 (mt) cc_final: 0.8206 (mt) REVERT: C 42 VAL cc_start: 0.9198 (m) cc_final: 0.8968 (m) REVERT: C 646 ARG cc_start: 0.7111 (tpt90) cc_final: 0.6836 (tpt-90) REVERT: C 867 ASP cc_start: 0.7910 (m-30) cc_final: 0.7628 (m-30) REVERT: C 902 MET cc_start: 0.8873 (tpt) cc_final: 0.8563 (tpt) REVERT: C 904 TYR cc_start: 0.6915 (t80) cc_final: 0.6679 (t80) outliers start: 14 outliers final: 4 residues processed: 272 average time/residue: 0.3490 time to fit residues: 148.0987 Evaluate side-chains 144 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 262 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 644 GLN A 655 HIS A 658 ASN A 755 GLN A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN A 957 GLN A 965 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS B 394 ASN B 542 ASN B 564 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 804 GLN B 901 GLN B 935 GLN B 954 GLN B 955 ASN B 965 GLN B1119 ASN C 536 ASN C 606 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 955 ASN C 965 GLN C1113 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23322 Z= 0.252 Angle : 0.692 14.122 31789 Z= 0.347 Chirality : 0.049 0.323 3889 Planarity : 0.004 0.051 4020 Dihedral : 8.052 58.973 4338 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.91 % Allowed : 8.69 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 2821 helix: 0.86 (0.20), residues: 675 sheet: -0.54 (0.21), residues: 539 loop : -1.30 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.006 0.001 HIS B 655 PHE 0.024 0.002 PHE A1042 TYR 0.030 0.002 TYR A1067 ARG 0.005 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 2.610 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.8696 (m-80) cc_final: 0.8491 (m-10) REVERT: B 353 TRP cc_start: 0.7978 (p-90) cc_final: 0.7717 (p-90) REVERT: B 562 PHE cc_start: 0.7223 (p90) cc_final: 0.6974 (p90) REVERT: B 1132 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8344 (pt) REVERT: C 200 TYR cc_start: 0.6751 (m-80) cc_final: 0.6461 (m-80) REVERT: C 525 CYS cc_start: 0.4863 (OUTLIER) cc_final: 0.4214 (m) REVERT: C 867 ASP cc_start: 0.7793 (m-30) cc_final: 0.7518 (m-30) REVERT: C 888 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8305 (p90) REVERT: C 904 TYR cc_start: 0.6953 (t80) cc_final: 0.6723 (t80) REVERT: C 1031 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7428 (mp0) outliers start: 45 outliers final: 14 residues processed: 198 average time/residue: 0.2965 time to fit residues: 97.3373 Evaluate side-chains 146 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 644 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 764 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23322 Z= 0.210 Angle : 0.617 13.300 31789 Z= 0.309 Chirality : 0.047 0.283 3889 Planarity : 0.004 0.045 4020 Dihedral : 7.477 58.263 4336 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.99 % Allowed : 11.44 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 2821 helix: 1.23 (0.21), residues: 667 sheet: -0.38 (0.21), residues: 567 loop : -1.25 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.017 0.001 PHE B 347 TYR 0.023 0.001 TYR C 170 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 2.924 Fit side-chains REVERT: A 515 PHE cc_start: 0.8737 (m-80) cc_final: 0.8474 (m-10) REVERT: B 562 PHE cc_start: 0.7299 (p90) cc_final: 0.7018 (p90) REVERT: B 1132 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8334 (pt) REVERT: C 200 TYR cc_start: 0.6729 (m-80) cc_final: 0.6527 (m-80) REVERT: C 306 PHE cc_start: 0.8116 (m-80) cc_final: 0.7823 (m-80) REVERT: C 525 CYS cc_start: 0.4875 (OUTLIER) cc_final: 0.4270 (m) REVERT: C 756 TYR cc_start: 0.8439 (m-10) cc_final: 0.8238 (m-10) REVERT: C 867 ASP cc_start: 0.7798 (m-30) cc_final: 0.7519 (m-30) REVERT: C 888 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8417 (p90) REVERT: C 904 TYR cc_start: 0.6898 (t80) cc_final: 0.6610 (t80) REVERT: C 1031 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7560 (mp0) outliers start: 47 outliers final: 16 residues processed: 192 average time/residue: 0.3118 time to fit residues: 100.3380 Evaluate side-chains 142 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 250 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 644 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 23322 Z= 0.295 Angle : 0.617 11.005 31789 Z= 0.309 Chirality : 0.047 0.287 3889 Planarity : 0.004 0.054 4020 Dihedral : 7.348 59.031 4336 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.99 % Allowed : 12.75 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2821 helix: 1.39 (0.21), residues: 646 sheet: -0.44 (0.21), residues: 591 loop : -1.18 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.005 0.001 HIS B 655 PHE 0.017 0.001 PHE B 643 TYR 0.021 0.001 TYR A1067 ARG 0.006 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.8805 (m-80) cc_final: 0.8452 (m-10) REVERT: B 133 PHE cc_start: 0.7056 (m-80) cc_final: 0.6779 (m-80) REVERT: B 562 PHE cc_start: 0.7356 (p90) cc_final: 0.6942 (p90) REVERT: B 1132 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8500 (pt) REVERT: C 200 TYR cc_start: 0.6719 (m-80) cc_final: 0.6480 (m-80) REVERT: C 306 PHE cc_start: 0.8129 (m-80) cc_final: 0.7873 (m-80) REVERT: C 525 CYS cc_start: 0.5090 (OUTLIER) cc_final: 0.4475 (m) REVERT: C 867 ASP cc_start: 0.7816 (m-30) cc_final: 0.7548 (m-30) REVERT: C 888 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8594 (p90) REVERT: C 904 TYR cc_start: 0.6963 (t80) cc_final: 0.6713 (t80) REVERT: C 1031 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7702 (mp0) outliers start: 47 outliers final: 23 residues processed: 173 average time/residue: 0.3061 time to fit residues: 88.8207 Evaluate side-chains 143 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 0.0270 chunk 158 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 250 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 23322 Z= 0.267 Angle : 0.595 9.641 31789 Z= 0.298 Chirality : 0.046 0.267 3889 Planarity : 0.004 0.062 4020 Dihedral : 7.190 58.295 4335 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.08 % Allowed : 13.73 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2821 helix: 1.38 (0.21), residues: 652 sheet: -0.47 (0.21), residues: 600 loop : -1.14 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 PHE 0.023 0.001 PHE A 374 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9068 (pttp) cc_final: 0.8852 (ptpp) REVERT: A 917 TYR cc_start: 0.8823 (m-80) cc_final: 0.8563 (m-80) REVERT: B 562 PHE cc_start: 0.7309 (p90) cc_final: 0.6889 (p90) REVERT: C 200 TYR cc_start: 0.6768 (m-80) cc_final: 0.6541 (m-80) REVERT: C 306 PHE cc_start: 0.8102 (m-80) cc_final: 0.7899 (m-80) REVERT: C 525 CYS cc_start: 0.5307 (OUTLIER) cc_final: 0.4685 (m) REVERT: C 773 GLU cc_start: 0.8202 (tt0) cc_final: 0.7986 (tt0) REVERT: C 867 ASP cc_start: 0.7792 (m-30) cc_final: 0.7512 (m-30) REVERT: C 904 TYR cc_start: 0.6944 (t80) cc_final: 0.6695 (t80) REVERT: C 940 SER cc_start: 0.8740 (m) cc_final: 0.8464 (p) REVERT: C 1031 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7729 (mp0) outliers start: 49 outliers final: 29 residues processed: 174 average time/residue: 0.2957 time to fit residues: 87.1058 Evaluate side-chains 142 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 146 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23322 Z= 0.183 Angle : 0.566 9.696 31789 Z= 0.283 Chirality : 0.045 0.264 3889 Planarity : 0.004 0.065 4020 Dihedral : 6.976 57.300 4335 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.86 % Allowed : 14.70 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2821 helix: 1.50 (0.21), residues: 650 sheet: -0.37 (0.21), residues: 590 loop : -1.12 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 PHE 0.018 0.001 PHE C 192 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 2.950 Fit side-chains revert: symmetry clash REVERT: A 1139 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7357 (p0) REVERT: B 562 PHE cc_start: 0.7258 (p90) cc_final: 0.6845 (p90) REVERT: C 392 PHE cc_start: 0.8394 (m-80) cc_final: 0.8187 (m-80) REVERT: C 505 TYR cc_start: 0.8546 (m-10) cc_final: 0.8239 (p90) REVERT: C 525 CYS cc_start: 0.5360 (OUTLIER) cc_final: 0.4747 (m) REVERT: C 598 ILE cc_start: 0.8547 (mm) cc_final: 0.8287 (mm) REVERT: C 867 ASP cc_start: 0.7753 (m-30) cc_final: 0.7470 (m-30) REVERT: C 904 TYR cc_start: 0.6857 (t80) cc_final: 0.6581 (t80) REVERT: C 940 SER cc_start: 0.8669 (m) cc_final: 0.8418 (p) REVERT: C 1031 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7706 (mp0) outliers start: 44 outliers final: 26 residues processed: 167 average time/residue: 0.2998 time to fit residues: 86.1320 Evaluate side-chains 149 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 644 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23322 Z= 0.396 Angle : 0.641 9.613 31789 Z= 0.321 Chirality : 0.047 0.270 3889 Planarity : 0.004 0.064 4020 Dihedral : 7.145 59.190 4335 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.25 % Allowed : 15.13 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2821 helix: 1.18 (0.21), residues: 664 sheet: -0.51 (0.21), residues: 628 loop : -1.19 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 886 HIS 0.006 0.001 HIS C1064 PHE 0.019 0.002 PHE C 377 TYR 0.023 0.001 TYR B 904 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 122 time to evaluate : 2.934 Fit side-chains revert: symmetry clash REVERT: A 1139 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7581 (p0) REVERT: B 562 PHE cc_start: 0.7421 (p90) cc_final: 0.6952 (p90) REVERT: B 740 MET cc_start: 0.8204 (tpp) cc_final: 0.7965 (tpp) REVERT: B 988 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7560 (pp20) REVERT: C 525 CYS cc_start: 0.5490 (OUTLIER) cc_final: 0.4861 (m) REVERT: C 596 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8674 (p) REVERT: C 867 ASP cc_start: 0.7778 (m-30) cc_final: 0.7536 (m-30) REVERT: C 904 TYR cc_start: 0.7087 (t80) cc_final: 0.6838 (t80) REVERT: C 940 SER cc_start: 0.8830 (m) cc_final: 0.8544 (p) REVERT: C 1031 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7856 (mp0) outliers start: 53 outliers final: 35 residues processed: 172 average time/residue: 0.3065 time to fit residues: 89.0890 Evaluate side-chains 153 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 113 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23322 Z= 0.184 Angle : 0.563 9.632 31789 Z= 0.281 Chirality : 0.045 0.267 3889 Planarity : 0.004 0.062 4020 Dihedral : 6.805 57.369 4335 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.82 % Allowed : 15.89 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2821 helix: 1.46 (0.21), residues: 657 sheet: -0.52 (0.21), residues: 612 loop : -1.06 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.002 0.001 HIS C1088 PHE 0.020 0.001 PHE C 192 TYR 0.021 0.001 TYR B 904 ARG 0.005 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 2.752 Fit side-chains revert: symmetry clash REVERT: A 1139 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7447 (p0) REVERT: B 562 PHE cc_start: 0.7196 (p90) cc_final: 0.6844 (p90) REVERT: B 1019 ARG cc_start: 0.8271 (tpp-160) cc_final: 0.8011 (tpp-160) REVERT: C 505 TYR cc_start: 0.8570 (m-10) cc_final: 0.8283 (p90) REVERT: C 596 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8640 (p) REVERT: C 598 ILE cc_start: 0.8574 (mm) cc_final: 0.8320 (mm) REVERT: C 867 ASP cc_start: 0.7723 (m-30) cc_final: 0.7441 (m-30) REVERT: C 904 TYR cc_start: 0.6892 (t80) cc_final: 0.6605 (t80) REVERT: C 940 SER cc_start: 0.8694 (m) cc_final: 0.8459 (p) REVERT: C 1031 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7784 (mp0) outliers start: 43 outliers final: 32 residues processed: 169 average time/residue: 0.3403 time to fit residues: 96.7783 Evaluate side-chains 151 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 243 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 258 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23322 Z= 0.202 Angle : 0.571 10.634 31789 Z= 0.283 Chirality : 0.045 0.264 3889 Planarity : 0.004 0.058 4020 Dihedral : 6.673 58.164 4334 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.95 % Allowed : 16.06 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2821 helix: 1.54 (0.21), residues: 658 sheet: -0.47 (0.21), residues: 618 loop : -1.05 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 PHE 0.017 0.001 PHE C 92 TYR 0.025 0.001 TYR B 904 ARG 0.006 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 123 time to evaluate : 2.877 Fit side-chains revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8283 (t0) cc_final: 0.8023 (t0) REVERT: A 1139 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7417 (p0) REVERT: B 562 PHE cc_start: 0.7212 (p90) cc_final: 0.6855 (p90) REVERT: B 1019 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.7996 (tpp-160) REVERT: C 505 TYR cc_start: 0.8569 (m-10) cc_final: 0.8280 (p90) REVERT: C 596 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8699 (p) REVERT: C 598 ILE cc_start: 0.8574 (mm) cc_final: 0.8304 (mm) REVERT: C 867 ASP cc_start: 0.7736 (m-30) cc_final: 0.7462 (m-30) REVERT: C 904 TYR cc_start: 0.6881 (t80) cc_final: 0.6587 (t80) REVERT: C 940 SER cc_start: 0.8682 (m) cc_final: 0.8453 (p) REVERT: C 1031 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7773 (mp0) outliers start: 46 outliers final: 34 residues processed: 165 average time/residue: 0.3035 time to fit residues: 84.1365 Evaluate side-chains 153 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 229 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23322 Z= 0.229 Angle : 0.578 9.617 31789 Z= 0.287 Chirality : 0.045 0.258 3889 Planarity : 0.004 0.058 4020 Dihedral : 6.608 57.163 4334 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.99 % Allowed : 16.10 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2821 helix: 1.59 (0.21), residues: 652 sheet: -0.49 (0.21), residues: 620 loop : -1.04 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 PHE 0.019 0.001 PHE B 855 TYR 0.025 0.001 TYR B 904 ARG 0.006 0.000 ARG C 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 125 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8268 (t0) cc_final: 0.8028 (t0) REVERT: A 1139 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7383 (p0) REVERT: B 562 PHE cc_start: 0.7218 (p90) cc_final: 0.6855 (p90) REVERT: B 1019 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.8007 (tpp-160) REVERT: C 200 TYR cc_start: 0.6661 (m-80) cc_final: 0.6449 (m-80) REVERT: C 505 TYR cc_start: 0.8578 (m-10) cc_final: 0.8282 (p90) REVERT: C 596 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8736 (p) REVERT: C 598 ILE cc_start: 0.8584 (mm) cc_final: 0.8317 (mm) REVERT: C 867 ASP cc_start: 0.7741 (m-30) cc_final: 0.7468 (m-30) REVERT: C 904 TYR cc_start: 0.6938 (t80) cc_final: 0.6704 (t80) REVERT: C 940 SER cc_start: 0.8687 (m) cc_final: 0.8463 (p) REVERT: C 1031 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: C 1050 MET cc_start: 0.7963 (mtp) cc_final: 0.7762 (mtp) outliers start: 47 outliers final: 35 residues processed: 166 average time/residue: 0.3124 time to fit residues: 87.0631 Evaluate side-chains 155 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 914 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 66 HIS C1010 GLN C1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.094366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064694 restraints weight = 60187.756| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.44 r_work: 0.2941 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.126 23322 Z= 0.594 Angle : 0.772 9.658 31789 Z= 0.388 Chirality : 0.050 0.273 3889 Planarity : 0.004 0.058 4020 Dihedral : 7.385 59.086 4334 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 2.08 % Allowed : 16.14 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 2821 helix: 0.83 (0.20), residues: 667 sheet: -0.73 (0.20), residues: 637 loop : -1.37 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 436 HIS 0.008 0.002 HIS C1064 PHE 0.025 0.002 PHE A1103 TYR 0.034 0.002 TYR B 904 ARG 0.006 0.001 ARG C 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4132.18 seconds wall clock time: 77 minutes 11.75 seconds (4631.75 seconds total)