Starting phenix.real_space_refine on Fri Mar 6 15:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7we9_32443/03_2026/7we9_32443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7we9_32443/03_2026/7we9_32443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7we9_32443/03_2026/7we9_32443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7we9_32443/03_2026/7we9_32443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7we9_32443/03_2026/7we9_32443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7we9_32443/03_2026/7we9_32443.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.073 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 138 5.16 5 C 20384 2.51 5 N 5260 2.21 5 O 6261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32043 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "F" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} 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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "Y" 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: "Z" 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: 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "F" 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: 8.14, per 1000 atoms: 0.25 Number of scatterers: 32043 At special positions: 0 Unit cell: (154.08, 178.69, 245.03, 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 138 16.00 O 6261 8.00 N 5260 7.00 C 20384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.02 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.02 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.02 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 134 " distance=2.03 Simple disulfide: pdb=" SG CYS F 129 " - pdb=" SG CYS F 161 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 298 " distance=2.03 Simple disulfide: pdb=" SG CYS F 333 " - pdb=" SG CYS F 358 " distance=2.03 Simple disulfide: pdb=" SG CYS F 376 " - pdb=" SG CYS F 429 " distance=2.03 Simple disulfide: pdb=" SG CYS F 388 " - pdb=" SG CYS F 522 " distance=2.03 Simple disulfide: pdb=" SG CYS F 477 " - pdb=" SG CYS F 485 " distance=2.03 Simple disulfide: pdb=" SG CYS F 614 " - pdb=" SG CYS F 646 " distance=2.03 Simple disulfide: pdb=" SG CYS F 659 " - pdb=" SG CYS F 668 " distance=2.03 Simple disulfide: pdb=" SG CYS F 735 " - pdb=" SG CYS F 757 " distance=2.03 Simple disulfide: pdb=" SG CYS F 740 " - pdb=" SG CYS F 746 " distance=2.03 Simple disulfide: pdb=" SG CYS F1029 " - pdb=" SG CYS F1040 " distance=2.03 Simple disulfide: pdb=" SG CYS F1079 " - pdb=" SG CYS F1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " NAG-ASN " NAG A1302 " - " ASN A1155 " " NAG A1303 " - " ASN A 143 " " NAG A1304 " - " ASN A 17 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 600 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 613 " " NAG A1309 " - " ASN A 706 " " NAG B1301 " - " ASN B1155 " " NAG B1302 " - " ASN B 123 " " NAG B1303 " - " ASN B 143 " " NAG B1304 " - " ASN B 17 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 600 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 706 " " NAG D 1 " - " ASN A 231 " " NAG E 1 " - " ASN A 328 " " NAG F1301 " - " ASN F1155 " " NAG F1302 " - " ASN F 123 " " NAG F1303 " - " ASN F 143 " " NAG F1304 " - " ASN F 17 " " NAG F1305 " - " ASN F 61 " " NAG F1306 " - " ASN F 600 " " NAG F1307 " - " ASN F 654 " " NAG F1308 " - " ASN F 613 " " NAG F1309 " - " ASN F 706 " " NAG G 1 " - " ASN A 714 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN A 798 " " NAG O 1 " - " ASN A1095 " " NAG P 1 " - " ASN A1131 " " NAG S 1 " - " ASN B 714 " " NAG U 1 " - " ASN B 798 " " NAG V 1 " - " ASN B1095 " " NAG W 1 " - " ASN B1131 " " NAG X 1 " - " ASN F 231 " " NAG Y 1 " - " ASN F 714 " " NAG a 1 " - " ASN F 798 " " NAG b 1 " - " ASN F1095 " " NAG c 1 " - " ASN F1131 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 58 sheets defined 19.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.680A pdb=" N LEU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.589A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.103A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.804A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.640A pdb=" N GLY A 636 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.605A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 750 Processing helix chain 'A' and resid 751 through 754 removed outlier: 3.661A pdb=" N GLY A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 756 through 771 removed outlier: 3.898A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 762 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 4.392A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 863 through 878 removed outlier: 3.696A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 918 through 928 removed outlier: 4.008A pdb=" N PHE A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 936 removed outlier: 4.329A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 removed outlier: 4.835A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 962 removed outlier: 3.528A pdb=" N ASN A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 974 through 979 removed outlier: 3.561A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1016 removed outlier: 4.236A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1026 Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 3.575A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1158 removed outlier: 4.819A pdb=" N TYR A1152 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE A1153 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS A1156 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A1157 " --> pdb=" O PHE A1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.522A pdb=" N LYS B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.771A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.154A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 4.208A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.849A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 777 removed outlier: 3.747A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 776 " --> pdb=" O ASP B 772 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 777 " --> pdb=" O LYS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 822 Processing helix chain 'B' and resid 847 through 851 removed outlier: 3.949A pdb=" N LYS B 851 " --> pdb=" O CYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 878 removed outlier: 3.521A pdb=" N GLY B 877 " --> pdb=" O ALA B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.593A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.520A pdb=" N MET B 899 " --> pdb=" O PHE B 895 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.672A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 928 removed outlier: 3.832A pdb=" N PHE B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 936 removed outlier: 4.330A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.068A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.915A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1019 removed outlier: 3.501A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1139 through 1153 removed outlier: 3.905A pdb=" N ASP B1143 " --> pdb=" O GLN B1139 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B1147 " --> pdb=" O ASP B1143 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU B1148 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B1153 " --> pdb=" O LEU B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1158 removed outlier: 3.824A pdb=" N THR B1157 " --> pdb=" O PHE B1153 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1153 through 1158' Processing helix chain 'F' and resid 291 through 299 Processing helix chain 'F' and resid 334 through 340 removed outlier: 4.251A pdb=" N VAL F 338 " --> pdb=" O PRO F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 368 Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.556A pdb=" N LEU F 384 " --> pdb=" O PRO F 381 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN F 385 " --> pdb=" O THR F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 408 removed outlier: 3.538A pdb=" N ILE F 407 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 408 " --> pdb=" O ARG F 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 404 through 408' Processing helix chain 'F' and resid 413 through 419 removed outlier: 3.725A pdb=" N TYR F 418 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN F 419 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 621 removed outlier: 4.020A pdb=" N VAL F 619 " --> pdb=" O THR F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 754 removed outlier: 3.953A pdb=" N LEU F 749 " --> pdb=" O GLU F 745 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR F 753 " --> pdb=" O LEU F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 754 through 779 removed outlier: 3.699A pdb=" N THR F 758 " --> pdb=" O GLY F 754 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 768 " --> pdb=" O LEU F 764 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU F 770 " --> pdb=" O GLY F 766 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP F 772 " --> pdb=" O ALA F 768 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR F 775 " --> pdb=" O GLN F 771 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU F 777 " --> pdb=" O LYS F 773 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE F 779 " --> pdb=" O THR F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 813 through 823 Processing helix chain 'F' and resid 863 through 881 Processing helix chain 'F' and resid 882 through 885 removed outlier: 4.247A pdb=" N PHE F 885 " --> pdb=" O GLY F 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 882 through 885' Processing helix chain 'F' and resid 898 through 903 Processing helix chain 'F' and resid 904 through 906 No H-bonds generated for 'chain 'F' and resid 904 through 906' Processing helix chain 'F' and resid 911 through 916 Processing helix chain 'F' and resid 916 through 936 removed outlier: 3.732A pdb=" N ASN F 925 " --> pdb=" O ALA F 921 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 927 " --> pdb=" O GLN F 923 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE F 928 " --> pdb=" O PHE F 924 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 929 " --> pdb=" O ASN F 925 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN F 932 " --> pdb=" O ILE F 928 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP F 933 " --> pdb=" O GLY F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 942 through 962 removed outlier: 3.869A pdb=" N GLN F 946 " --> pdb=" O LEU F 942 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP F 947 " --> pdb=" O GLY F 943 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL F 948 " --> pdb=" O LYS F 944 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU F 956 " --> pdb=" O ASN F 952 " (cutoff:3.500A) Processing helix chain 'F' and resid 963 through 965 No H-bonds generated for 'chain 'F' and resid 963 through 965' Processing helix chain 'F' and resid 973 through 979 removed outlier: 3.581A pdb=" N ILE F 977 " --> pdb=" O VAL F 973 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE F 978 " --> pdb=" O LEU F 974 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER F 979 " --> pdb=" O ASN F 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 973 through 979' Processing helix chain 'F' and resid 982 through 1026 removed outlier: 4.012A pdb=" N GLU F 987 " --> pdb=" O LYS F 983 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL F 988 " --> pdb=" O VAL F 984 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN F 989 " --> pdb=" O GLU F 985 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 993 " --> pdb=" O GLN F 989 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F1004 " --> pdb=" O SER F1000 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE F1010 " --> pdb=" O THR F1006 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA F1017 " --> pdb=" O ALA F1013 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA F1023 " --> pdb=" O ALA F1019 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR F1024 " --> pdb=" O ASN F1020 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET F1026 " --> pdb=" O ALA F1022 " (cutoff:3.500A) Processing helix chain 'F' and resid 1113 through 1115 No H-bonds generated for 'chain 'F' and resid 1113 through 1115' Processing helix chain 'F' and resid 1139 through 1157 removed outlier: 4.480A pdb=" N SER F1144 " --> pdb=" O PRO F1140 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE F1145 " --> pdb=" O GLU F1141 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS F1146 " --> pdb=" O LEU F1142 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU F1147 " --> pdb=" O ASP F1143 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU F1148 " --> pdb=" O SER F1144 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F1149 " --> pdb=" O PHE F1145 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS F1151 " --> pdb=" O GLU F1147 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR F1152 " --> pdb=" O GLU F1148 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE F1153 " --> pdb=" O LEU F1149 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS F1154 " --> pdb=" O ASP F1150 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN F1155 " --> pdb=" O LYS F1151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS F1156 " --> pdb=" O TYR F1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.531A pdb=" N SER C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.084A pdb=" N THR C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.544A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.867A pdb=" N ARG H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.618A pdb=" N THR I 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 4.081A pdb=" N GLU K 84 " --> pdb=" O SER K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.689A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.618A pdb=" N VAL A 47 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.506A pdb=" N GLN A 236 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 103 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 312 removed outlier: 4.272A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.705A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 399 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN A 434 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N PHE A 371 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA7, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.848A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 548 through 551 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 642 removed outlier: 3.843A pdb=" N GLY A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 652 removed outlier: 3.590A pdb=" N GLU A 651 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 691 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 700 through 701 removed outlier: 7.318A pdb=" N ASN A 700 " --> pdb=" O LYS F 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.927A pdb=" N ILE A 709 " --> pdb=" O PHE A1072 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A1072 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 711 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 716 Processing sheet with id=AB5, first strand: chain 'A' and resid 719 through 725 removed outlier: 3.807A pdb=" N THR A 720 " --> pdb=" O HIS A1061 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A1053 " --> pdb=" O GLY A1056 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 732 removed outlier: 3.512A pdb=" N SER A 732 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.072A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 261 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 224 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.817A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.329A pdb=" N LEU B 82 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE B 235 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 126 through 129 Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.806A pdb=" N THR B 596 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 315 through 316 Processing sheet with id=AC5, first strand: chain 'B' and resid 321 through 325 removed outlier: 7.689A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 353 through 355 removed outlier: 4.202A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 509 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 399 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 432 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.686A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 521 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC9, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.507A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 583 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 562 through 564 removed outlier: 4.267A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 661 through 662 removed outlier: 3.805A pdb=" N ILE B 661 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 709 through 712 removed outlier: 3.536A pdb=" N LYS B1070 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 724 removed outlier: 3.761A pdb=" N PHE B1049 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B1062 " --> pdb=" O MET B1047 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1078 through 1079 Processing sheet with id=AD6, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD7, first strand: chain 'F' and resid 27 through 31 removed outlier: 3.805A pdb=" N SER F 60 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN F 61 " --> pdb=" O TYR F 266 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR F 266 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 261 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER F 200 " --> pdb=" O PRO F 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 48 through 55 removed outlier: 3.818A pdb=" N ASP F 284 " --> pdb=" O LYS F 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AE1, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.836A pdb=" N PHE F 163 " --> pdb=" O VAL F 128 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 308 through 316 removed outlier: 4.040A pdb=" N THR F 596 " --> pdb=" O GLY F 308 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL F 592 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASN F 314 " --> pdb=" O GLY F 590 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY F 590 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 351 through 355 removed outlier: 3.837A pdb=" N ASN F 351 " --> pdb=" O SER F 396 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 392 " --> pdb=" O ILE F 355 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 358 through 359 removed outlier: 6.752A pdb=" N CYS F 358 " --> pdb=" O CYS F 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'F' and resid 548 through 551 removed outlier: 3.640A pdb=" N VAL F 548 " --> pdb=" O THR F 585 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR F 585 " --> pdb=" O VAL F 548 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 651 through 652 removed outlier: 3.621A pdb=" N GLU F 651 " --> pdb=" O ILE F 689 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 691 " --> pdb=" O GLU F 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 688 " --> pdb=" O GLN F 672 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN F 672 " --> pdb=" O SER F 688 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA F 669 " --> pdb=" O PRO F 662 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 720 through 724 removed outlier: 3.702A pdb=" N MET F1047 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR F1064 " --> pdb=" O HIS F1045 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS F1045 " --> pdb=" O TYR F1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 1073 through 1074 removed outlier: 4.034A pdb=" N THR F1073 " --> pdb=" O SER F1094 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F1094 " --> pdb=" O THR F1073 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 1117 through 1122 removed outlier: 5.193A pdb=" N ALA F1084 " --> pdb=" O SER F1120 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS F1079 " --> pdb=" O VAL F1130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.965A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 72 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.458A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 5 through 6 removed outlier: 4.041A pdb=" N TYR H 79 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.692A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'I' and resid 57 through 58 removed outlier: 6.608A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.753A pdb=" N VAL J 18 " --> pdb=" O ILE J 76 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 49 through 50 removed outlier: 4.165A pdb=" N VAL J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG1, first strand: chain 'K' and resid 46 through 50 removed outlier: 5.606A pdb=" N LEU K 47 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN K 38 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA K 91 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL K 102 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.839A pdb=" N VAL L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.775A pdb=" N VAL L 102 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 17 through 23 849 hydrogen bonds defined for protein. 2196 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: 7.27 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10050 1.34 - 1.46: 8268 1.46 - 1.59: 14301 1.59 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 32796 Sorted by residual: bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1 NAG F1305 " pdb=" O5 NAG F1305 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 32791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 43670 2.19 - 4.37: 851 4.37 - 6.56: 87 6.56 - 8.74: 16 8.74 - 10.93: 2 Bond angle restraints: 44626 Sorted by residual: angle pdb=" N VAL A 617 " pdb=" CA VAL A 617 " pdb=" CB VAL A 617 " ideal model delta sigma weight residual 110.50 115.05 -4.55 6.30e-01 2.52e+00 5.22e+01 angle pdb=" N ASN F 541 " pdb=" CA ASN F 541 " pdb=" C ASN F 541 " ideal model delta sigma weight residual 110.91 118.69 -7.78 1.17e+00 7.31e-01 4.43e+01 angle pdb=" O ASP B 136 " pdb=" C ASP B 136 " pdb=" N PRO B 137 " ideal model delta sigma weight residual 121.37 116.10 5.27 9.00e-01 1.23e+00 3.43e+01 angle pdb=" C GLU A 321 " pdb=" N SER A 322 " pdb=" CA SER A 322 " ideal model delta sigma weight residual 122.59 113.40 9.19 1.57e+00 4.06e-01 3.42e+01 angle pdb=" CA ASP B 136 " pdb=" C ASP B 136 " pdb=" N PRO B 137 " ideal model delta sigma weight residual 117.75 122.57 -4.82 9.90e-01 1.02e+00 2.37e+01 ... (remaining 44621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 18983 23.84 - 47.68: 1132 47.68 - 71.52: 145 71.52 - 95.35: 79 95.35 - 119.19: 54 Dihedral angle restraints: 20393 sinusoidal: 8834 harmonic: 11559 Sorted by residual: dihedral pdb=" CA ASP F 140 " pdb=" C ASP F 140 " pdb=" N HIS F 141 " pdb=" CA HIS F 141 " ideal model delta harmonic sigma weight residual 180.00 120.75 59.25 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CB CYS F1029 " pdb=" SG CYS F1029 " pdb=" SG CYS F1040 " pdb=" CB CYS F1040 " ideal model delta sinusoidal sigma weight residual 93.00 -179.14 -87.86 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 1.73 -87.73 1 1.00e+01 1.00e-02 9.22e+01 ... (remaining 20390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 5133 0.130 - 0.260: 62 0.260 - 0.390: 8 0.390 - 0.520: 2 0.520 - 0.650: 1 Chirality restraints: 5206 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN F1131 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A 798 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 5203 not shown) Planarity restraints: 5701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 789 " 0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO F 790 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO F 790 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 790 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " 0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO L 8 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 203 " 0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO F 204 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 204 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 204 " 0.043 5.00e-02 4.00e+02 ... (remaining 5698 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 761 2.67 - 3.23: 30671 3.23 - 3.79: 45202 3.79 - 4.34: 60124 4.34 - 4.90: 97885 Nonbonded interactions: 234643 Sorted by model distance: nonbonded pdb=" O GLY A 877 " pdb=" OG SER A 881 " model vdw 2.118 3.040 nonbonded pdb=" O ALA A1023 " pdb=" OG SER A1027 " model vdw 2.145 3.040 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.147 3.040 nonbonded pdb=" O ALA F 876 " pdb=" OG1 THR F 880 " model vdw 2.154 3.040 nonbonded pdb=" O GLU B 658 " pdb=" OH TYR B 692 " model vdw 2.159 3.040 ... (remaining 234638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'W' selection = chain 'b' selection = chain 'c' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.690 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.150 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 0.084 32910 Z= 0.235 Angle : 0.724 12.224 44917 Z= 0.376 Chirality : 0.051 0.650 5206 Planarity : 0.004 0.095 5659 Dihedral : 16.563 119.193 12842 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.16 % Favored : 91.71 % Rotamer: Outliers : 0.17 % Allowed : 0.58 % Favored : 99.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 3945 helix: -1.90 (0.19), residues: 618 sheet: -0.36 (0.19), residues: 792 loop : -1.74 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1104 TYR 0.021 0.001 TYR F 377 PHE 0.019 0.001 PHE A1106 TRP 0.020 0.001 TRP C 36 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd covalent geometry : bond 0.00460 (32796) covalent geometry : angle 0.70329 (44626) SS BOND : bond 0.00376 ( 45) SS BOND : angle 1.56346 ( 90) hydrogen bonds : bond 0.26113 ( 843) hydrogen bonds : angle 8.78608 ( 2196) Misc. bond : bond 0.00143 ( 2) link_BETA1-4 : bond 0.00535 ( 25) link_BETA1-4 : angle 1.64047 ( 75) link_NAG-ASN : bond 0.00660 ( 42) link_NAG-ASN : angle 2.84767 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 261 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 THR cc_start: 0.5672 (OUTLIER) cc_final: 0.5308 (t) REVERT: A 495 ARG cc_start: 0.7529 (mmp80) cc_final: 0.7198 (mmm160) REVERT: F 52 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8059 (tm-30) REVERT: F 172 MET cc_start: 0.3554 (mmp) cc_final: 0.2721 (mpp) REVERT: F 193 ASP cc_start: 0.8569 (t70) cc_final: 0.8106 (t70) outliers start: 6 outliers final: 2 residues processed: 267 average time/residue: 0.1900 time to fit residues: 84.2688 Evaluate side-chains 213 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 672 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 314 ASN A 367 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A1020 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.171623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128087 restraints weight = 76701.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129805 restraints weight = 50805.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.130018 restraints weight = 37013.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.130705 restraints weight = 33551.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.131313 restraints weight = 31099.687| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32910 Z= 0.131 Angle : 0.655 13.331 44917 Z= 0.322 Chirality : 0.048 0.385 5206 Planarity : 0.004 0.067 5659 Dihedral : 12.556 115.006 5788 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 0.44 % Allowed : 7.27 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.13), residues: 3945 helix: -1.50 (0.19), residues: 656 sheet: -0.26 (0.20), residues: 738 loop : -1.78 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 208 TYR 0.025 0.001 TYR F 704 PHE 0.019 0.001 PHE B1118 TRP 0.018 0.001 TRP C 106 HIS 0.006 0.001 HIS F1098 Details of bonding type rmsd covalent geometry : bond 0.00285 (32796) covalent geometry : angle 0.63058 (44626) SS BOND : bond 0.00327 ( 45) SS BOND : angle 1.16491 ( 90) hydrogen bonds : bond 0.05659 ( 843) hydrogen bonds : angle 6.25153 ( 2196) Misc. bond : bond 0.00069 ( 2) link_BETA1-4 : bond 0.00658 ( 25) link_BETA1-4 : angle 2.13218 ( 75) link_NAG-ASN : bond 0.00615 ( 42) link_NAG-ASN : angle 2.93067 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 320 THR cc_start: 0.5375 (OUTLIER) cc_final: 0.5153 (t) REVERT: A 495 ARG cc_start: 0.7552 (mmp80) cc_final: 0.7255 (mmm160) REVERT: F 395 ASP cc_start: 0.8295 (m-30) cc_final: 0.8015 (m-30) REVERT: F 1014 GLU cc_start: 0.7297 (pt0) cc_final: 0.7094 (pt0) REVERT: I 80 MET cc_start: 0.0364 (mpp) cc_final: -0.0459 (tmm) outliers start: 15 outliers final: 8 residues processed: 243 average time/residue: 0.2002 time to fit residues: 80.6592 Evaluate side-chains 215 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain F residue 311 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 246 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 237 optimal weight: 0.3980 chunk 35 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 284 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 305 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 351 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 951 HIS A 952 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.171498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.127344 restraints weight = 78797.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.129858 restraints weight = 51915.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.130375 restraints weight = 34457.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.130826 restraints weight = 31310.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.131252 restraints weight = 29319.759| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32910 Z= 0.122 Angle : 0.617 13.254 44917 Z= 0.299 Chirality : 0.047 0.385 5206 Planarity : 0.004 0.060 5659 Dihedral : 10.613 116.001 5785 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.54 % Rotamer: Outliers : 0.81 % Allowed : 10.67 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.13), residues: 3945 helix: -1.26 (0.19), residues: 666 sheet: -0.34 (0.19), residues: 774 loop : -1.71 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 451 TYR 0.019 0.001 TYR F 704 PHE 0.026 0.001 PHE A 756 TRP 0.012 0.001 TRP L 101 HIS 0.004 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00274 (32796) covalent geometry : angle 0.59139 (44626) SS BOND : bond 0.00284 ( 45) SS BOND : angle 1.09580 ( 90) hydrogen bonds : bond 0.04746 ( 843) hydrogen bonds : angle 5.76455 ( 2196) Misc. bond : bond 0.00166 ( 2) link_BETA1-4 : bond 0.00640 ( 25) link_BETA1-4 : angle 2.16524 ( 75) link_NAG-ASN : bond 0.00598 ( 42) link_NAG-ASN : angle 2.85479 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 ARG cc_start: 0.7486 (mmp80) cc_final: 0.7231 (mmm160) REVERT: F 148 MET cc_start: 0.3775 (mtm) cc_final: 0.3409 (ttp) REVERT: F 395 ASP cc_start: 0.8198 (m-30) cc_final: 0.7996 (m-30) REVERT: C 48 MET cc_start: 0.6559 (tpp) cc_final: 0.6133 (mmm) REVERT: C 63 PHE cc_start: 0.7412 (m-10) cc_final: 0.7205 (m-80) REVERT: C 69 MET cc_start: 0.7235 (tpp) cc_final: 0.6956 (tpp) REVERT: C 79 TYR cc_start: 0.7509 (m-80) cc_final: 0.7216 (m-80) REVERT: I 80 MET cc_start: 0.0401 (mpp) cc_final: -0.0315 (tmm) REVERT: K 47 LEU cc_start: 0.5204 (tp) cc_final: 0.4956 (tp) REVERT: L 32 ASN cc_start: 0.8584 (p0) cc_final: 0.8219 (p0) REVERT: L 67 LYS cc_start: 0.8611 (mttt) cc_final: 0.8355 (mttt) outliers start: 28 outliers final: 11 residues processed: 256 average time/residue: 0.1937 time to fit residues: 82.0473 Evaluate side-chains 224 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain C residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 187 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 360 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 245 optimal weight: 6.9990 chunk 292 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A1051 GLN A1103 GLN B 113 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN B 892 GLN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.169361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.126913 restraints weight = 76277.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.127764 restraints weight = 54351.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.128137 restraints weight = 38353.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.128382 restraints weight = 39188.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128516 restraints weight = 34379.613| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32910 Z= 0.182 Angle : 0.667 14.939 44917 Z= 0.326 Chirality : 0.048 0.401 5206 Planarity : 0.004 0.057 5659 Dihedral : 9.612 113.509 5784 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.86 % Favored : 92.04 % Rotamer: Outliers : 1.77 % Allowed : 12.53 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.13), residues: 3945 helix: -1.30 (0.19), residues: 662 sheet: -0.43 (0.19), residues: 778 loop : -1.81 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 325 TYR 0.024 0.002 TYR A1064 PHE 0.023 0.002 PHE B1118 TRP 0.014 0.001 TRP B1099 HIS 0.005 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00425 (32796) covalent geometry : angle 0.63911 (44626) SS BOND : bond 0.00345 ( 45) SS BOND : angle 1.32965 ( 90) hydrogen bonds : bond 0.04835 ( 843) hydrogen bonds : angle 5.78626 ( 2196) Misc. bond : bond 0.00169 ( 2) link_BETA1-4 : bond 0.00561 ( 25) link_BETA1-4 : angle 2.24981 ( 75) link_NAG-ASN : bond 0.00565 ( 42) link_NAG-ASN : angle 3.08991 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 221 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 495 ARG cc_start: 0.7452 (mmp80) cc_final: 0.7234 (mmm160) REVERT: A 541 ASN cc_start: 0.8001 (m-40) cc_final: 0.7272 (p0) REVERT: F 148 MET cc_start: 0.3696 (mtm) cc_final: 0.3281 (ttp) REVERT: C 48 MET cc_start: 0.6732 (tpp) cc_final: 0.6377 (mmm) REVERT: C 69 MET cc_start: 0.7120 (tpp) cc_final: 0.6830 (tpp) REVERT: C 80 MET cc_start: 0.4754 (ttp) cc_final: 0.4257 (ttm) REVERT: K 47 LEU cc_start: 0.5070 (tp) cc_final: 0.4795 (tp) REVERT: L 32 ASN cc_start: 0.8441 (p0) cc_final: 0.8236 (p0) outliers start: 61 outliers final: 35 residues processed: 272 average time/residue: 0.1879 time to fit residues: 85.0858 Evaluate side-chains 234 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 PHE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 638 ASN Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 704 TYR Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 361 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 346 optimal weight: 40.0000 chunk 212 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 219 optimal weight: 6.9990 chunk 328 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 952 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.174341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.146099 restraints weight = 78059.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.142819 restraints weight = 78554.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.144782 restraints weight = 73895.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.144470 restraints weight = 49740.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.146477 restraints weight = 44588.263| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32910 Z= 0.135 Angle : 0.635 12.993 44917 Z= 0.307 Chirality : 0.047 0.389 5206 Planarity : 0.004 0.062 5659 Dihedral : 8.913 112.184 5784 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.44 % Favored : 93.46 % Rotamer: Outliers : 1.77 % Allowed : 14.36 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 3945 helix: -1.16 (0.19), residues: 665 sheet: -0.40 (0.19), residues: 790 loop : -1.77 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 997 TYR 0.016 0.001 TYR F 704 PHE 0.017 0.001 PHE B1118 TRP 0.013 0.001 TRP L 101 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd covalent geometry : bond 0.00312 (32796) covalent geometry : angle 0.60737 (44626) SS BOND : bond 0.00315 ( 45) SS BOND : angle 1.29240 ( 90) hydrogen bonds : bond 0.04303 ( 843) hydrogen bonds : angle 5.60432 ( 2196) Misc. bond : bond 0.00105 ( 2) link_BETA1-4 : bond 0.00551 ( 25) link_BETA1-4 : angle 2.23240 ( 75) link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 2.96458 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 1.195 Fit side-chains REVERT: A 541 ASN cc_start: 0.7254 (m-40) cc_final: 0.6893 (p0) REVERT: A 874 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6657 (mm) REVERT: A 1031 LEU cc_start: 0.7630 (mt) cc_final: 0.7414 (mt) REVERT: B 1104 ARG cc_start: 0.7350 (mmm160) cc_final: 0.7142 (mmt180) REVERT: F 148 MET cc_start: 0.3685 (mtm) cc_final: 0.3237 (ttp) REVERT: F 172 MET cc_start: 0.3280 (mmp) cc_final: 0.2424 (mpp) REVERT: F 981 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7933 (pp) REVERT: F 1010 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8505 (mt) REVERT: C 48 MET cc_start: 0.6354 (tpp) cc_final: 0.6152 (mmm) REVERT: C 69 MET cc_start: 0.6835 (tpp) cc_final: 0.6488 (tpp) REVERT: I 48 MET cc_start: 0.3159 (mtm) cc_final: 0.1912 (tmm) REVERT: I 80 MET cc_start: 0.1509 (mpp) cc_final: 0.0302 (tmm) REVERT: K 47 LEU cc_start: 0.4450 (tp) cc_final: 0.4017 (tp) outliers start: 61 outliers final: 41 residues processed: 266 average time/residue: 0.1878 time to fit residues: 83.7451 Evaluate side-chains 249 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 981 LEU Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 246 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 146 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 372 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 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 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 952 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.175634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.147293 restraints weight = 77744.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.144519 restraints weight = 82901.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.145827 restraints weight = 70905.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.145911 restraints weight = 55122.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.148002 restraints weight = 45396.037| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32910 Z= 0.107 Angle : 0.607 12.916 44917 Z= 0.293 Chirality : 0.046 0.382 5206 Planarity : 0.004 0.063 5659 Dihedral : 8.255 110.244 5784 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.16 % Favored : 93.74 % Rotamer: Outliers : 1.86 % Allowed : 15.14 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.13), residues: 3945 helix: -0.94 (0.20), residues: 662 sheet: -0.33 (0.19), residues: 748 loop : -1.68 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 451 TYR 0.016 0.001 TYR F 704 PHE 0.017 0.001 PHE F 90 TRP 0.013 0.001 TRP L 101 HIS 0.004 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00238 (32796) covalent geometry : angle 0.58063 (44626) SS BOND : bond 0.00265 ( 45) SS BOND : angle 1.06256 ( 90) hydrogen bonds : bond 0.03861 ( 843) hydrogen bonds : angle 5.37967 ( 2196) Misc. bond : bond 0.00066 ( 2) link_BETA1-4 : bond 0.00583 ( 25) link_BETA1-4 : angle 2.21549 ( 75) link_NAG-ASN : bond 0.00642 ( 42) link_NAG-ASN : angle 2.89277 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 541 ASN cc_start: 0.7190 (m-40) cc_final: 0.6887 (p0) REVERT: A 874 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6639 (mm) REVERT: A 1031 LEU cc_start: 0.7630 (mt) cc_final: 0.7423 (mt) REVERT: F 148 MET cc_start: 0.3559 (mtm) cc_final: 0.3142 (ttp) REVERT: F 1010 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8465 (mt) REVERT: C 39 GLN cc_start: 0.6537 (tt0) cc_final: 0.6332 (tt0) REVERT: C 45 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6780 (mt) REVERT: C 69 MET cc_start: 0.6832 (tpp) cc_final: 0.6511 (tpp) REVERT: I 48 MET cc_start: 0.3278 (mtm) cc_final: 0.2020 (tmm) REVERT: I 80 MET cc_start: 0.1576 (mpp) cc_final: 0.0485 (tmm) REVERT: K 47 LEU cc_start: 0.4346 (tp) cc_final: 0.3908 (tp) outliers start: 64 outliers final: 42 residues processed: 275 average time/residue: 0.1874 time to fit residues: 86.6731 Evaluate side-chains 250 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 638 ASN Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain I residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 159 optimal weight: 3.9990 chunk 355 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 313 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 390 optimal weight: 9.9990 chunk 386 optimal weight: 7.9990 chunk 348 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN B 141 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN B 672 GLN B 781 GLN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.173950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.131625 restraints weight = 79642.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.130241 restraints weight = 53204.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.129992 restraints weight = 43298.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.130412 restraints weight = 39994.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.130536 restraints weight = 37423.653| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 32910 Z= 0.282 Angle : 0.760 13.335 44917 Z= 0.379 Chirality : 0.051 0.411 5206 Planarity : 0.005 0.074 5659 Dihedral : 8.476 106.586 5784 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.53 % Favored : 90.37 % Rotamer: Outliers : 2.62 % Allowed : 15.29 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.13), residues: 3945 helix: -1.32 (0.19), residues: 641 sheet: -0.61 (0.19), residues: 819 loop : -1.92 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 997 TYR 0.036 0.002 TYR A1064 PHE 0.031 0.002 PHE F 187 TRP 0.020 0.002 TRP B1099 HIS 0.007 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00662 (32796) covalent geometry : angle 0.73657 (44626) SS BOND : bond 0.00525 ( 45) SS BOND : angle 1.75220 ( 90) hydrogen bonds : bond 0.05342 ( 843) hydrogen bonds : angle 5.90740 ( 2196) Misc. bond : bond 0.00036 ( 2) link_BETA1-4 : bond 0.00519 ( 25) link_BETA1-4 : angle 2.27817 ( 75) link_NAG-ASN : bond 0.00632 ( 42) link_NAG-ASN : angle 2.94113 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 212 time to evaluate : 1.230 Fit side-chains REVERT: A 417 ASP cc_start: 0.7110 (m-30) cc_final: 0.6903 (m-30) REVERT: A 541 ASN cc_start: 0.8050 (m-40) cc_final: 0.7208 (p0) REVERT: A 874 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6853 (mm) REVERT: B 108 LEU cc_start: 0.5313 (mp) cc_final: 0.4717 (tp) REVERT: F 148 MET cc_start: 0.3873 (mtm) cc_final: 0.3396 (ttp) REVERT: F 172 MET cc_start: 0.3437 (mmp) cc_final: 0.2794 (mpp) REVERT: F 344 PHE cc_start: 0.1697 (OUTLIER) cc_final: 0.0481 (m-80) REVERT: F 704 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6490 (t80) REVERT: F 895 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7202 (t80) REVERT: F 1010 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8770 (mt) REVERT: C 69 MET cc_start: 0.7135 (tpp) cc_final: 0.6714 (tpp) REVERT: C 79 TYR cc_start: 0.7591 (m-80) cc_final: 0.7351 (m-80) REVERT: I 48 MET cc_start: 0.4017 (mtm) cc_final: 0.2321 (tmm) outliers start: 90 outliers final: 59 residues processed: 289 average time/residue: 0.1834 time to fit residues: 90.0393 Evaluate side-chains 269 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 PHE Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 344 PHE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 638 ASN Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 704 TYR Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1063 THR Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 361 optimal weight: 30.0000 chunk 330 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 318 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 952 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN B 781 GLN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.177219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.149716 restraints weight = 79106.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.145754 restraints weight = 91908.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.147158 restraints weight = 82507.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.147868 restraints weight = 58170.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.147933 restraints weight = 53825.493| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32910 Z= 0.126 Angle : 0.638 12.701 44917 Z= 0.311 Chirality : 0.047 0.384 5206 Planarity : 0.004 0.063 5659 Dihedral : 7.888 104.269 5783 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 1.95 % Allowed : 16.33 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.13), residues: 3945 helix: -1.05 (0.19), residues: 658 sheet: -0.49 (0.19), residues: 754 loop : -1.77 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 631 TYR 0.023 0.001 TYR F 450 PHE 0.019 0.001 PHE B 43 TRP 0.016 0.001 TRP L 101 HIS 0.004 0.001 HIS F1098 Details of bonding type rmsd covalent geometry : bond 0.00288 (32796) covalent geometry : angle 0.61336 (44626) SS BOND : bond 0.00395 ( 45) SS BOND : angle 1.40651 ( 90) hydrogen bonds : bond 0.04117 ( 843) hydrogen bonds : angle 5.51907 ( 2196) Misc. bond : bond 0.00031 ( 2) link_BETA1-4 : bond 0.00541 ( 25) link_BETA1-4 : angle 2.13646 ( 75) link_NAG-ASN : bond 0.00571 ( 42) link_NAG-ASN : angle 2.80861 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 1.196 Fit side-chains REVERT: A 417 ASP cc_start: 0.6947 (m-30) cc_final: 0.6737 (m-30) REVERT: A 541 ASN cc_start: 0.7562 (m-40) cc_final: 0.7034 (p0) REVERT: A 874 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6619 (mm) REVERT: A 1031 LEU cc_start: 0.7646 (mt) cc_final: 0.7419 (mt) REVERT: F 148 MET cc_start: 0.3715 (mtm) cc_final: 0.3176 (ttp) REVERT: F 172 MET cc_start: 0.3462 (mmp) cc_final: 0.1957 (mmt) REVERT: F 897 MET cc_start: 0.5793 (pmm) cc_final: 0.5304 (ptt) REVERT: F 1010 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8511 (mt) REVERT: C 69 MET cc_start: 0.6768 (tpp) cc_final: 0.6389 (tpp) REVERT: I 48 MET cc_start: 0.3464 (mtm) cc_final: 0.2120 (tmm) REVERT: K 47 LEU cc_start: 0.4605 (tp) cc_final: 0.4224 (tp) outliers start: 67 outliers final: 54 residues processed: 276 average time/residue: 0.1876 time to fit residues: 87.1031 Evaluate side-chains 260 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 638 ASN Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain I residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 102 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 200 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 393 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 372 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 134 optimal weight: 0.4980 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 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 952 ASN B 672 GLN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 952 ASN ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.174667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.145630 restraints weight = 77656.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.142309 restraints weight = 73951.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.143623 restraints weight = 67199.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.144215 restraints weight = 46548.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.144927 restraints weight = 42767.681| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32910 Z= 0.109 Angle : 0.618 12.722 44917 Z= 0.300 Chirality : 0.046 0.376 5206 Planarity : 0.004 0.061 5659 Dihedral : 7.414 99.295 5783 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.11 % Rotamer: Outliers : 1.95 % Allowed : 16.62 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.13), residues: 3945 helix: -0.85 (0.20), residues: 658 sheet: -0.32 (0.19), residues: 753 loop : -1.69 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 451 TYR 0.021 0.001 TYR F 450 PHE 0.020 0.001 PHE B 181 TRP 0.018 0.001 TRP K 36 HIS 0.005 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00246 (32796) covalent geometry : angle 0.59309 (44626) SS BOND : bond 0.00297 ( 45) SS BOND : angle 1.20710 ( 90) hydrogen bonds : bond 0.03717 ( 843) hydrogen bonds : angle 5.28747 ( 2196) Misc. bond : bond 0.00022 ( 2) link_BETA1-4 : bond 0.00529 ( 25) link_BETA1-4 : angle 2.11300 ( 75) link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 2.77544 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 215 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 541 ASN cc_start: 0.7380 (m-40) cc_final: 0.6950 (p0) REVERT: A 874 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6665 (mm) REVERT: A 1031 LEU cc_start: 0.7676 (mt) cc_final: 0.7473 (mt) REVERT: F 148 MET cc_start: 0.3674 (mtm) cc_final: 0.3204 (ttp) REVERT: F 172 MET cc_start: 0.3289 (mmp) cc_final: 0.1852 (mmt) REVERT: F 1010 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8486 (mt) REVERT: C 69 MET cc_start: 0.6791 (tpp) cc_final: 0.6479 (tpp) REVERT: I 48 MET cc_start: 0.3588 (mtm) cc_final: 0.2146 (tmm) REVERT: K 47 LEU cc_start: 0.4473 (tp) cc_final: 0.4052 (tp) outliers start: 67 outliers final: 53 residues processed: 275 average time/residue: 0.1916 time to fit residues: 88.6508 Evaluate side-chains 269 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 638 ASN Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 275 optimal weight: 4.9990 chunk 333 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 351 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 952 ASN B 672 GLN ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.176699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.149427 restraints weight = 79415.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.144130 restraints weight = 81967.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.145535 restraints weight = 87727.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.146150 restraints weight = 60303.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.146425 restraints weight = 52777.249| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32910 Z= 0.153 Angle : 0.648 12.895 44917 Z= 0.316 Chirality : 0.047 0.383 5206 Planarity : 0.004 0.058 5659 Dihedral : 7.344 94.948 5783 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.45 % Favored : 92.45 % Rotamer: Outliers : 2.01 % Allowed : 16.71 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 3945 helix: -0.88 (0.20), residues: 656 sheet: -0.44 (0.19), residues: 759 loop : -1.72 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 400 TYR 0.023 0.001 TYR B 165 PHE 0.020 0.001 PHE B1118 TRP 0.018 0.001 TRP K 36 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00359 (32796) covalent geometry : angle 0.62417 (44626) SS BOND : bond 0.00329 ( 45) SS BOND : angle 1.35111 ( 90) hydrogen bonds : bond 0.04080 ( 843) hydrogen bonds : angle 5.37498 ( 2196) Misc. bond : bond 0.00019 ( 2) link_BETA1-4 : bond 0.00504 ( 25) link_BETA1-4 : angle 2.11958 ( 75) link_NAG-ASN : bond 0.00557 ( 42) link_NAG-ASN : angle 2.80887 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 1.197 Fit side-chains REVERT: A 541 ASN cc_start: 0.7585 (m-40) cc_final: 0.7015 (p0) REVERT: A 874 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6784 (mm) REVERT: A 1031 LEU cc_start: 0.7811 (mt) cc_final: 0.7566 (mt) REVERT: B 108 LEU cc_start: 0.4694 (mp) cc_final: 0.4266 (tp) REVERT: F 148 MET cc_start: 0.3834 (mtm) cc_final: 0.3309 (ttp) REVERT: F 172 MET cc_start: 0.3456 (mmp) cc_final: 0.2061 (mmt) REVERT: F 895 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.6990 (t80) REVERT: F 1010 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8561 (mt) REVERT: C 69 MET cc_start: 0.6782 (tpp) cc_final: 0.6469 (tpp) REVERT: I 48 MET cc_start: 0.4067 (mtm) cc_final: 0.2325 (tmm) REVERT: K 47 LEU cc_start: 0.4853 (tp) cc_final: 0.4500 (tp) outliers start: 69 outliers final: 60 residues processed: 276 average time/residue: 0.1844 time to fit residues: 86.4603 Evaluate side-chains 271 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 638 ASN Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 365 optimal weight: 30.0000 chunk 218 optimal weight: 40.0000 chunk 225 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 157 optimal weight: 0.0050 chunk 283 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 260 optimal weight: 0.7980 chunk 287 optimal weight: 4.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN B 180 ASN B 672 GLN ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.174023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.146116 restraints weight = 78123.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.143900 restraints weight = 85039.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.145192 restraints weight = 71932.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.146409 restraints weight = 46881.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.146494 restraints weight = 44442.679| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32910 Z= 0.125 Angle : 0.636 12.834 44917 Z= 0.309 Chirality : 0.046 0.386 5206 Planarity : 0.004 0.054 5659 Dihedral : 7.139 91.067 5783 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.87 % Favored : 93.03 % Rotamer: Outliers : 1.89 % Allowed : 17.00 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.13), residues: 3945 helix: -0.79 (0.20), residues: 658 sheet: -0.42 (0.20), residues: 741 loop : -1.67 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 451 TYR 0.019 0.001 TYR F 450 PHE 0.040 0.001 PHE B 181 TRP 0.022 0.001 TRP F 102 HIS 0.004 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00292 (32796) covalent geometry : angle 0.61279 (44626) SS BOND : bond 0.00298 ( 45) SS BOND : angle 1.22078 ( 90) hydrogen bonds : bond 0.03850 ( 843) hydrogen bonds : angle 5.29361 ( 2196) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00518 ( 25) link_BETA1-4 : angle 2.08023 ( 75) link_NAG-ASN : bond 0.00549 ( 42) link_NAG-ASN : angle 2.74148 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5610.84 seconds wall clock time: 97 minutes 57.06 seconds (5877.06 seconds total)