Starting phenix.real_space_refine on Mon Jul 6 02:44:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7we9_32443/07_2026/7we9_32443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7we9_32443/07_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_32443/07_2026/7we9_32443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7we9_32443/07_2026/7we9_32443.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7we9_32443/07_2026/7we9_32443.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7we9_32443/07_2026/7we9_32443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7we9_32443/07_2026/7we9_32443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7we9_32443/07_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-6108/lib/python3.11/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 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 chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 9 Time building chain proxies: 5.76, per 1000 atoms: 0.18 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: 2.42 Conformation dependent library (CDL) restraints added in 1.4 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: 1.18 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: 6.67 Time building geometry restraints manager: 3.26 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 - 17.78: 17028 17.78 - 35.55: 1533 35.55 - 53.33: 258 53.33 - 71.11: 39 71.11 - 88.88: 33 Dihedral angle restraints: 18891 sinusoidal: 7332 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 18888 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: 0.02 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.800 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 13.751 88.881 11340 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/Z covalent geometry : bond 0.00460 / 0.23 (32796) covalent geometry : angle 0.70329 / 0.37 (44626) SS BOND : bond 0.00376 / 0.27 ( 45) SS BOND : angle 1.56346 / 1.02 ( 90) hydrogen bonds : bond 0.26113 / 16.56 ( 843) hydrogen bonds : angle 8.78608 / 6.02 ( 2196) Misc. bond : bond 0.00143 / 0.08 ( 2) link_BETA1-4 : bond 0.00535 / 0.35 ( 25) link_BETA1-4 : angle 1.64047 / 1.08 ( 75) link_NAG-ASN : bond 0.00660 / 0.50 ( 42) link_NAG-ASN : angle 2.84767 / 1.94 ( 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 : 0.737 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: 0.1728 time to fit residues: 76.7828 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 : 1.072 ------------------------------------------------------------------------------- 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... 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 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.171814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.128632 restraints weight = 76669.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.129604 restraints weight = 51605.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.130283 restraints weight = 41247.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.131303 restraints weight = 33334.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.131375 restraints weight = 31204.700| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1015 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= 0.129 Angle : 0.631 13.427 44917 Z= 0.316 Chirality : 0.047 0.397 5206 Planarity : 0.004 0.067 5659 Dihedral : 4.900 50.531 4286 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 0.46 % Allowed : 7.38 % Favored : 92.15 % 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: -2.09 (0.13), residues: 3945 helix: -1.52 (0.19), residues: 656 sheet: -0.27 (0.20), residues: 738 loop : -1.78 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 208 TYR 0.024 0.001 TYR F 704 PHE 0.020 0.001 PHE B1118 TRP 0.017 0.001 TRP C 106 HIS 0.006 0.001 HIS F1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (32796) covalent geometry : angle 0.61014 / 0.31 (44626) SS BOND : bond 0.00324 / 0.23 ( 45) SS BOND : angle 1.16912 / 0.76 ( 90) hydrogen bonds : bond 0.05683 / 3.74 ( 843) hydrogen bonds : angle 6.25898 / 4.29 ( 2196) Misc. bond : bond 0.00135 / 0.07 ( 2) link_BETA1-4 : bond 0.00684 / 0.44 ( 25) link_BETA1-4 : angle 1.56231 / 1.03 ( 75) link_NAG-ASN : bond 0.00618 / 0.44 ( 42) link_NAG-ASN : angle 2.79610 / 1.83 ( 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 248 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 320 THR cc_start: 0.5339 (OUTLIER) cc_final: 0.5113 (t) REVERT: A 495 ARG cc_start: 0.7554 (mmp80) cc_final: 0.7253 (mmm160) REVERT: F 395 ASP cc_start: 0.8292 (m-30) cc_final: 0.8013 (m-30) REVERT: F 899 MET cc_start: 0.8025 (mmt) cc_final: 0.7683 (mmp) REVERT: F 1014 GLU cc_start: 0.7206 (pt0) cc_final: 0.7001 (pt0) REVERT: I 80 MET cc_start: 0.0349 (mpp) cc_final: -0.0468 (tmm) outliers start: 16 outliers final: 8 residues processed: 244 average time/residue: 0.1764 time to fit residues: 71.6441 Evaluate side-chains 216 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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: 0.9990 chunk 115 optimal weight: 0.0970 chunk 237 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 351 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.4528 r_free = 0.4528 target = 0.171693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.128897 restraints weight = 76751.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.129861 restraints weight = 58193.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.129883 restraints weight = 46070.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.130597 restraints weight = 39067.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.130972 restraints weight = 35340.794| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1258 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= 0.120 Angle : 0.589 13.373 44917 Z= 0.293 Chirality : 0.046 0.378 5206 Planarity : 0.004 0.062 5659 Dihedral : 4.664 50.524 4283 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 0.70 % Allowed : 10.55 % Favored : 88.75 % 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: -1.98 (0.13), residues: 3945 helix: -1.29 (0.19), residues: 667 sheet: -0.35 (0.19), residues: 774 loop : -1.71 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1088 TYR 0.019 0.001 TYR F 704 PHE 0.021 0.001 PHE A 640 TRP 0.012 0.001 TRP L 101 HIS 0.004 0.001 HIS B 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (32796) covalent geometry : angle 0.56808 / 0.29 (44626) SS BOND : bond 0.00283 / 0.19 ( 45) SS BOND : angle 1.08442 / 0.72 ( 90) hydrogen bonds : bond 0.04793 / 3.18 ( 843) hydrogen bonds : angle 5.80685 / 3.98 ( 2196) Misc. bond : bond 0.00192 / 0.10 ( 2) link_BETA1-4 : bond 0.00586 / 0.36 ( 25) link_BETA1-4 : angle 1.48984 / 0.98 ( 75) link_NAG-ASN : bond 0.00589 / 0.41 ( 42) link_NAG-ASN : angle 2.70671 / 1.77 ( 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 256 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 ARG cc_start: 0.7485 (mmp80) cc_final: 0.7230 (mmm160) REVERT: F 148 MET cc_start: 0.3803 (mtm) cc_final: 0.3422 (ttp) REVERT: C 48 MET cc_start: 0.6581 (tpp) cc_final: 0.6157 (mmm) REVERT: C 63 PHE cc_start: 0.7245 (m-10) cc_final: 0.7006 (m-80) REVERT: C 69 MET cc_start: 0.7225 (tpp) cc_final: 0.6932 (tpp) REVERT: C 79 TYR cc_start: 0.7523 (m-80) cc_final: 0.7221 (m-80) REVERT: I 80 MET cc_start: 0.0460 (mpp) cc_final: -0.0421 (tmm) REVERT: K 47 LEU cc_start: 0.5155 (tp) cc_final: 0.4894 (tp) REVERT: L 32 ASN cc_start: 0.8608 (p0) cc_final: 0.8259 (p0) REVERT: L 67 LYS cc_start: 0.8601 (mttt) cc_final: 0.8337 (mttt) outliers start: 24 outliers final: 9 residues processed: 253 average time/residue: 0.1753 time to fit residues: 72.7346 Evaluate side-chains 220 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 F residue 326 PHE Chi-restraints excluded: chain F residue 539 ASN 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: 9.9990 chunk 298 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 360 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 334 optimal weight: 8.9990 chunk 240 optimal weight: 20.0000 chunk 248 optimal weight: 0.2980 chunk 245 optimal weight: 5.9990 chunk 292 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.170148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.126369 restraints weight = 78208.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.127937 restraints weight = 54758.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128314 restraints weight = 39492.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.129192 restraints weight = 34127.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.129528 restraints weight = 31357.028| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32910 Z= 0.151 Angle : 0.614 13.497 44917 Z= 0.305 Chirality : 0.047 0.404 5206 Planarity : 0.004 0.058 5659 Dihedral : 4.722 48.516 4282 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.38 % Favored : 92.52 % Rotamer: Outliers : 1.66 % Allowed : 12.44 % Favored : 85.91 % 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: -1.20 (0.19), residues: 663 sheet: -0.37 (0.20), residues: 760 loop : -1.75 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 451 TYR 0.020 0.001 TYR A1064 PHE 0.020 0.001 PHE B1118 TRP 0.012 0.001 TRP L 101 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (32796) covalent geometry : angle 0.59098 / 0.30 (44626) SS BOND : bond 0.00329 / 0.22 ( 45) SS BOND : angle 1.30972 / 0.83 ( 90) hydrogen bonds : bond 0.04579 / 3.03 ( 843) hydrogen bonds : angle 5.68086 / 3.89 ( 2196) Misc. bond : bond 0.00161 / 0.08 ( 2) link_BETA1-4 : bond 0.00555 / 0.34 ( 25) link_BETA1-4 : angle 1.47408 / 0.98 ( 75) link_NAG-ASN : bond 0.00575 / 0.41 ( 42) link_NAG-ASN : angle 2.82953 / 1.84 ( 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 281 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 ARG cc_start: 0.7476 (mmp80) cc_final: 0.7189 (mmm160) REVERT: F 148 MET cc_start: 0.3738 (mtm) cc_final: 0.3335 (ttp) REVERT: F 899 MET cc_start: 0.7951 (mmt) cc_final: 0.7562 (mmp) REVERT: C 48 MET cc_start: 0.6716 (tpp) cc_final: 0.6396 (mmm) REVERT: C 69 MET cc_start: 0.7260 (tpp) cc_final: 0.6975 (tpp) REVERT: C 79 TYR cc_start: 0.7288 (m-80) cc_final: 0.7022 (m-80) REVERT: I 80 MET cc_start: 0.0548 (mpp) cc_final: -0.0176 (tmm) REVERT: K 47 LEU cc_start: 0.5171 (tp) cc_final: 0.4930 (tp) REVERT: L 32 ASN cc_start: 0.8478 (p0) cc_final: 0.8201 (p0) REVERT: L 67 LYS cc_start: 0.8601 (mttt) cc_final: 0.8301 (mttt) outliers start: 57 outliers final: 31 residues processed: 274 average time/residue: 0.1716 time to fit residues: 78.4341 Evaluate side-chains 234 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 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 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 906 ILE Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 361 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 346 optimal weight: 20.0000 chunk 212 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 262 optimal weight: 0.4980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.175848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.133982 restraints weight = 79827.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.133440 restraints weight = 53150.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.133107 restraints weight = 41243.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.133584 restraints weight = 40173.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.133729 restraints weight = 35691.195| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32910 Z= 0.190 Angle : 0.655 12.965 44917 Z= 0.327 Chirality : 0.048 0.441 5206 Planarity : 0.004 0.062 5659 Dihedral : 4.960 49.526 4282 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 2.15 % Allowed : 13.98 % 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: -2.08 (0.13), residues: 3945 helix: -1.25 (0.19), residues: 658 sheet: -0.49 (0.19), residues: 795 loop : -1.80 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 997 TYR 0.030 0.002 TYR A 657 PHE 0.023 0.002 PHE B1118 TRP 0.014 0.001 TRP B1099 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (32796) covalent geometry : angle 0.63375 / 0.32 (44626) SS BOND : bond 0.00408 / 0.27 ( 45) SS BOND : angle 1.49393 / 0.98 ( 90) hydrogen bonds : bond 0.04748 / 3.16 ( 843) hydrogen bonds : angle 5.74353 / 3.94 ( 2196) Misc. bond : bond 0.00147 / 0.08 ( 2) link_BETA1-4 : bond 0.00549 / 0.34 ( 25) link_BETA1-4 : angle 1.48137 / 0.99 ( 75) link_NAG-ASN : bond 0.00588 / 0.41 ( 42) link_NAG-ASN : angle 2.75249 / 1.82 ( 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 288 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 214 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 495 ARG cc_start: 0.7447 (mmp80) cc_final: 0.7178 (mmm160) REVERT: A 541 ASN cc_start: 0.7998 (m-40) cc_final: 0.7262 (p0) REVERT: A 874 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6742 (mm) REVERT: F 148 MET cc_start: 0.3926 (mtm) cc_final: 0.3451 (ttp) REVERT: F 172 MET cc_start: 0.3335 (mmp) cc_final: 0.2598 (mpp) REVERT: F 895 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7219 (t80) REVERT: F 981 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8006 (pp) REVERT: F 1010 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8547 (mt) REVERT: C 45 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6833 (mt) REVERT: C 48 MET cc_start: 0.6402 (tpp) cc_final: 0.6191 (mmm) REVERT: C 69 MET cc_start: 0.7270 (tpp) cc_final: 0.6870 (tpp) REVERT: I 48 MET cc_start: 0.4073 (mtm) cc_final: 0.2296 (tmm) REVERT: K 47 LEU cc_start: 0.5433 (tp) cc_final: 0.5197 (tp) REVERT: L 32 ASN cc_start: 0.8471 (p0) cc_final: 0.8215 (p0) REVERT: L 67 LYS cc_start: 0.8537 (mttt) cc_final: 0.8205 (mttt) outliers start: 74 outliers final: 44 residues processed: 278 average time/residue: 0.1713 time to fit residues: 79.6516 Evaluate side-chains 257 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 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 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 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 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 508 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 875 LEU 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 C residue 45 LEU 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: 5.9990 chunk 31 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 372 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 = 0.4661 r_free = 0.4661 target = 0.177723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.150892 restraints weight = 78807.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.146442 restraints weight = 88780.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.147991 restraints weight = 84890.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.148556 restraints weight = 58293.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.148957 restraints weight = 52990.621| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32910 Z= 0.127 Angle : 0.604 13.084 44917 Z= 0.299 Chirality : 0.046 0.396 5206 Planarity : 0.004 0.064 5659 Dihedral : 4.722 46.846 4282 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.54 % Favored : 93.36 % Rotamer: Outliers : 2.06 % Allowed : 15.49 % Favored : 82.45 % 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: -1.98 (0.13), residues: 3945 helix: -1.09 (0.19), residues: 663 sheet: -0.51 (0.19), residues: 779 loop : -1.72 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 451 TYR 0.019 0.001 TYR A 657 PHE 0.018 0.001 PHE B 43 TRP 0.014 0.001 TRP L 101 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (32796) covalent geometry : angle 0.58692 / 0.30 (44626) SS BOND : bond 0.00285 / 0.19 ( 45) SS BOND : angle 1.19278 / 0.78 ( 90) hydrogen bonds : bond 0.04160 / 2.77 ( 843) hydrogen bonds : angle 5.54042 / 3.79 ( 2196) Misc. bond : bond 0.00229 / 0.12 ( 2) link_BETA1-4 : bond 0.00572 / 0.34 ( 25) link_BETA1-4 : angle 1.43412 / 0.94 ( 75) link_NAG-ASN : bond 0.00663 / 0.49 ( 42) link_NAG-ASN : angle 2.39986 / 1.64 ( 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 286 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 215 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ASN cc_start: 0.7440 (m-40) cc_final: 0.6965 (p0) REVERT: A 874 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6668 (mm) REVERT: A 1031 LEU cc_start: 0.7731 (mt) cc_final: 0.7503 (mt) REVERT: F 148 MET cc_start: 0.3744 (mtm) cc_final: 0.3278 (ttp) REVERT: F 895 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6881 (t80) REVERT: F 1010 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8563 (mt) REVERT: C 69 MET cc_start: 0.6855 (tpp) cc_final: 0.6457 (tpp) REVERT: I 48 MET cc_start: 0.3616 (mtm) cc_final: 0.2124 (tmm) REVERT: K 47 LEU cc_start: 0.4629 (tp) cc_final: 0.4227 (tp) REVERT: L 67 LYS cc_start: 0.8225 (mttt) cc_final: 0.7881 (mttt) outliers start: 71 outliers final: 44 residues processed: 280 average time/residue: 0.1666 time to fit residues: 78.8061 Evaluate side-chains 252 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 874 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 53 ASP 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 579 LEU 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 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 123 ASN Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 271 THR 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 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 875 LEU 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 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: 0.8980 chunk 355 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 313 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 3 optimal weight: 0.0770 chunk 390 optimal weight: 10.0000 chunk 386 optimal weight: 0.8980 chunk 348 optimal weight: 6.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.174800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.146214 restraints weight = 78061.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.144079 restraints weight = 78092.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.145531 restraints weight = 70061.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.145520 restraints weight = 47387.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.147128 restraints weight = 42967.335| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32910 Z= 0.116 Angle : 0.595 12.722 44917 Z= 0.294 Chirality : 0.046 0.368 5206 Planarity : 0.004 0.062 5659 Dihedral : 4.576 47.373 4282 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Rotamer: Outliers : 1.92 % Allowed : 15.90 % Favored : 82.19 % 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: -0.91 (0.20), residues: 662 sheet: -0.40 (0.19), residues: 768 loop : -1.66 (0.12), residues: 2515 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 0.018 0.001 PHE B 43 TRP 0.014 0.001 TRP K 36 HIS 0.003 0.001 HIS F1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (32796) covalent geometry : angle 0.57800 / 0.29 (44626) SS BOND : bond 0.00366 / 0.25 ( 45) SS BOND : angle 1.18714 / 0.76 ( 90) hydrogen bonds : bond 0.03882 / 2.59 ( 843) hydrogen bonds : angle 5.36119 / 3.67 ( 2196) Misc. bond : bond 0.00091 / 0.05 ( 2) link_BETA1-4 : bond 0.00556 / 0.33 ( 25) link_BETA1-4 : angle 1.39687 / 0.92 ( 75) link_NAG-ASN : bond 0.00577 / 0.41 ( 42) link_NAG-ASN : angle 2.35011 / 1.61 ( 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 282 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 216 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ASN cc_start: 0.7213 (m-40) cc_final: 0.6866 (p0) REVERT: A 874 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6558 (mm) REVERT: A 1031 LEU cc_start: 0.7525 (mt) cc_final: 0.7323 (mt) REVERT: F 148 MET cc_start: 0.3606 (mtm) cc_final: 0.3182 (ttp) REVERT: F 172 MET cc_start: 0.3405 (mmp) cc_final: 0.2501 (mpp) REVERT: F 1010 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8519 (mt) REVERT: C 69 MET cc_start: 0.6750 (tpp) cc_final: 0.6421 (tpp) REVERT: I 48 MET cc_start: 0.3443 (mtm) cc_final: 0.2156 (tmm) REVERT: K 47 LEU cc_start: 0.4327 (tp) cc_final: 0.3895 (tp) REVERT: L 67 LYS cc_start: 0.8161 (mttt) cc_final: 0.7952 (mttt) outliers start: 66 outliers final: 49 residues processed: 276 average time/residue: 0.1725 time to fit residues: 79.7031 Evaluate side-chains 259 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 594 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 702 VAL 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 53 ASP 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 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 579 LEU 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 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 1063 THR 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 548 VAL Chi-restraints excluded: chain F residue 617 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 875 LEU 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 1063 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 361 optimal weight: 30.0000 chunk 330 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 318 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 242 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN B 141 HIS ** 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** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.175666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.134110 restraints weight = 79775.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.131860 restraints weight = 52419.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.132593 restraints weight = 48900.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.132813 restraints weight = 38610.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.133214 restraints weight = 36366.567| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32910 Z= 0.185 Angle : 0.672 23.141 44917 Z= 0.331 Chirality : 0.049 0.580 5206 Planarity : 0.004 0.064 5659 Dihedral : 4.850 56.416 4281 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.09 % Favored : 91.81 % Rotamer: Outliers : 2.32 % Allowed : 16.10 % Favored : 81.58 % 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: -1.99 (0.13), residues: 3945 helix: -1.05 (0.19), residues: 661 sheet: -0.46 (0.19), residues: 781 loop : -1.76 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.023 0.002 TYR A1064 PHE 0.036 0.002 PHE F 187 TRP 0.016 0.001 TRP B1099 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (32796) covalent geometry : angle 0.63740 / 0.32 (44626) SS BOND : bond 0.00373 / 0.24 ( 45) SS BOND : angle 1.51404 / 0.99 ( 90) hydrogen bonds : bond 0.04393 / 2.94 ( 843) hydrogen bonds : angle 5.52776 / 3.78 ( 2196) Misc. bond : bond 0.00372 / 0.20 ( 2) link_BETA1-4 : bond 0.00534 / 0.33 ( 25) link_BETA1-4 : angle 1.43736 / 0.96 ( 75) link_NAG-ASN : bond 0.00719 / 0.55 ( 42) link_NAG-ASN : angle 3.75011 / 2.12 ( 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 288 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 208 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7135 (m-30) cc_final: 0.6859 (m-30) REVERT: A 541 ASN cc_start: 0.8003 (m-40) cc_final: 0.7251 (p0) REVERT: A 874 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6758 (mm) REVERT: F 148 MET cc_start: 0.3834 (mtm) cc_final: 0.3355 (ttp) REVERT: F 172 MET cc_start: 0.3397 (mmp) cc_final: 0.1927 (mmt) REVERT: F 188 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8353 (p) REVERT: F 344 PHE cc_start: 0.1457 (OUTLIER) cc_final: 0.0221 (m-80) REVERT: F 895 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7180 (t80) REVERT: F 1010 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8569 (mt) REVERT: C 69 MET cc_start: 0.7172 (tpp) cc_final: 0.6887 (tpp) REVERT: C 79 TYR cc_start: 0.7260 (m-80) cc_final: 0.7047 (m-80) REVERT: K 47 LEU cc_start: 0.5309 (tp) cc_final: 0.5059 (tp) REVERT: L 67 LYS cc_start: 0.8556 (mttt) cc_final: 0.8337 (mttt) outliers start: 80 outliers final: 64 residues processed: 275 average time/residue: 0.1703 time to fit residues: 78.9939 Evaluate side-chains 272 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 203 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 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 702 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 913 LEU 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 51 THR 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 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 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 1063 THR Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 PHE Chi-restraints excluded: chain F residue 188 VAL 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 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 875 LEU 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 1026 MET 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 C residue 80 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 102 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 393 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 268 optimal weight: 0.9980 chunk 372 optimal weight: 0.4980 chunk 213 optimal weight: 0.0060 chunk 134 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** A 391 ASN ** 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** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.174996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.147197 restraints weight = 77732.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.145031 restraints weight = 82993.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.146626 restraints weight = 72301.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.146497 restraints weight = 49627.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.148163 restraints weight = 43641.222| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2113 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= 0.108 Angle : 0.607 14.504 44917 Z= 0.297 Chirality : 0.046 0.475 5206 Planarity : 0.004 0.062 5659 Dihedral : 4.542 53.468 4281 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.91 % Favored : 93.99 % Rotamer: Outliers : 1.63 % Allowed : 17.15 % Favored : 81.23 % 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: -1.81 (0.13), residues: 3945 helix: -0.80 (0.20), residues: 665 sheet: -0.35 (0.19), residues: 768 loop : -1.66 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 451 TYR 0.017 0.001 TYR F 704 PHE 0.029 0.001 PHE A 756 TRP 0.018 0.001 TRP K 36 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (32796) covalent geometry : angle 0.58196 / 0.29 (44626) SS BOND : bond 0.00282 / 0.20 ( 45) SS BOND : angle 1.19934 / 0.76 ( 90) hydrogen bonds : bond 0.03662 / 2.45 ( 843) hydrogen bonds : angle 5.26093 / 3.60 ( 2196) Misc. bond : bond 0.00321 / 0.17 ( 2) link_BETA1-4 : bond 0.00558 / 0.33 ( 25) link_BETA1-4 : angle 1.36686 / 0.89 ( 75) link_NAG-ASN : bond 0.00569 / 0.40 ( 42) link_NAG-ASN : angle 3.00923 / 1.82 ( 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 280 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 541 ASN cc_start: 0.7103 (m-40) cc_final: 0.6814 (p0) REVERT: A 874 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6540 (mm) REVERT: B 971 SER cc_start: 0.8621 (t) cc_final: 0.8332 (m) REVERT: F 148 MET cc_start: 0.3596 (mtm) cc_final: 0.3166 (ttp) REVERT: F 172 MET cc_start: 0.3511 (mmp) cc_final: 0.2062 (mmt) REVERT: C 69 MET cc_start: 0.6525 (tpp) cc_final: 0.6307 (tpp) REVERT: I 48 MET cc_start: 0.2639 (mtm) cc_final: 0.1822 (tmm) REVERT: K 47 LEU cc_start: 0.4088 (tp) cc_final: 0.3652 (tp) outliers start: 56 outliers final: 45 residues processed: 275 average time/residue: 0.1682 time to fit residues: 77.9562 Evaluate side-chains 260 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR 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 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR 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 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 948 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 195 TYR 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 539 ASN Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 875 LEU 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 1063 THR Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL 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: 5.9990 chunk 333 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 351 optimal weight: 0.0970 chunk 160 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.175137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.145872 restraints weight = 78353.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143213 restraints weight = 69531.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.144392 restraints weight = 69002.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.144513 restraints weight = 49849.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.145408 restraints weight = 43299.759| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 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 0.044 32910 Z= 0.108 Angle : 0.601 12.839 44917 Z= 0.295 Chirality : 0.046 0.365 5206 Planarity : 0.004 0.060 5659 Dihedral : 4.471 49.651 4281 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.54 % Rotamer: Outliers : 1.54 % Allowed : 17.47 % Favored : 80.99 % 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: -1.76 (0.13), residues: 3945 helix: -0.73 (0.20), residues: 670 sheet: -0.30 (0.19), residues: 750 loop : -1.64 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1104 TYR 0.020 0.001 TYR A 704 PHE 0.039 0.001 PHE A 756 TRP 0.020 0.001 TRP K 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (32796) covalent geometry : angle 0.58008 / 0.29 (44626) SS BOND : bond 0.00315 / 0.22 ( 45) SS BOND : angle 1.17872 / 0.75 ( 90) hydrogen bonds : bond 0.03550 / 2.37 ( 843) hydrogen bonds : angle 5.16907 / 3.54 ( 2196) Misc. bond : bond 0.00254 / 0.13 ( 2) link_BETA1-4 : bond 0.00543 / 0.32 ( 25) link_BETA1-4 : angle 1.35408 / 0.89 ( 75) link_NAG-ASN : bond 0.00565 / 0.40 ( 42) link_NAG-ASN : angle 2.76007 / 1.74 ( 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 274 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 874 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6594 (mm) REVERT: F 148 MET cc_start: 0.3822 (mtm) cc_final: 0.3396 (ttp) REVERT: F 172 MET cc_start: 0.3590 (mmp) cc_final: 0.2221 (mmt) REVERT: I 48 MET cc_start: 0.2803 (mtm) cc_final: 0.2047 (tmm) REVERT: K 47 LEU cc_start: 0.4356 (tp) cc_final: 0.4002 (tp) outliers start: 53 outliers final: 49 residues processed: 268 average time/residue: 0.1659 time to fit residues: 74.6902 Evaluate side-chains 265 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR 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 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 486 TYR 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 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 F residue 195 TYR 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 632 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 875 LEU 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 1063 THR 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 365 optimal weight: 30.0000 chunk 218 optimal weight: 40.0000 chunk 225 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 157 optimal weight: 0.3980 chunk 283 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN B 672 GLN B 781 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** C 6 GLN ** 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 = 0.4561 r_free = 0.4561 target = 0.173973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.131307 restraints weight = 79910.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.130779 restraints weight = 54348.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.130587 restraints weight = 42061.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.131114 restraints weight = 41397.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.131360 restraints weight = 36448.539| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 32910 Z= 0.260 Angle : 0.750 18.204 44917 Z= 0.376 Chirality : 0.051 0.456 5206 Planarity : 0.005 0.068 5659 Dihedral : 5.174 43.398 4281 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.95 % Favored : 90.95 % Rotamer: Outliers : 2.01 % Allowed : 17.26 % Favored : 80.73 % 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: -2.10 (0.13), residues: 3945 helix: -1.16 (0.19), residues: 659 sheet: -0.44 (0.19), residues: 783 loop : -1.86 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.032 0.002 TYR A1064 PHE 0.036 0.002 PHE A 756 TRP 0.019 0.002 TRP B1099 HIS 0.006 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.26 (32796) covalent geometry : angle 0.72816 / 0.37 (44626) SS BOND : bond 0.00468 / 0.29 ( 45) SS BOND : angle 1.78839 / 1.18 ( 90) hydrogen bonds : bond 0.05058 / 3.39 ( 843) hydrogen bonds : angle 5.68734 / 3.90 ( 2196) Misc. bond : bond 0.00474 / 0.25 ( 2) link_BETA1-4 : bond 0.00564 / 0.34 ( 25) link_BETA1-4 : angle 1.49024 / 1.00 ( 75) link_NAG-ASN : bond 0.00648 / 0.47 ( 42) link_NAG-ASN : angle 3.05136 / 1.96 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5097.77 seconds wall clock time: 89 minutes 2.21 seconds (5342.21 seconds total)