Starting phenix.real_space_refine on Tue Aug 26 00:05:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzi_27799/08_2025/8dzi_27799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzi_27799/08_2025/8dzi_27799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dzi_27799/08_2025/8dzi_27799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzi_27799/08_2025/8dzi_27799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dzi_27799/08_2025/8dzi_27799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzi_27799/08_2025/8dzi_27799.map" } resolution = 3.5 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= 0.001 sd= 0.003 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 20037 2.51 5 N 5161 2.21 5 O 6134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31470 Number of models: 1 Model: "" Number of chains: 32 Chain: "C" Number of atoms: 8496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8496 Classifications: {'peptide': 1083} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1022} Chain breaks: 9 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 8467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8467 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 59, 'TRANS': 1020} Chain breaks: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 8420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8420 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 59, 'TRANS': 1014} Chain breaks: 8 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "G" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 8.44, per 1000 atoms: 0.27 Number of scatterers: 31470 At special positions: 0 Unit cell: (177.62, 146.59, 218.28, 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 6134 8.00 N 5161 7.00 C 20037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.04 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 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=2.03 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 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 298 " distance=2.02 Simple disulfide: pdb=" SG CYS E 333 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 376 " - pdb=" SG CYS E 429 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 522 " distance=2.03 Simple disulfide: pdb=" SG CYS E 477 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS E 535 " - pdb=" SG CYS E 587 " distance=2.03 Simple disulfide: pdb=" SG CYS E 614 " - pdb=" SG CYS E 646 " distance=2.03 Simple disulfide: pdb=" SG CYS E 659 " - pdb=" SG CYS E 668 " distance=2.04 Simple disulfide: pdb=" SG CYS E 735 " - pdb=" SG CYS E 757 " distance=2.03 Simple disulfide: pdb=" SG CYS E 740 " - pdb=" SG CYS E 746 " distance=2.03 Simple disulfide: pdb=" SG CYS E 837 " - pdb=" SG CYS E 848 " distance=2.03 Simple disulfide: pdb=" SG CYS E1029 " - pdb=" SG CYS E1040 " distance=2.03 Simple disulfide: pdb=" SG CYS E1079 " - pdb=" SG CYS E1123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " 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=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " 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 c 1 " - " NAG c 2 " NAG-ASN " NAG A1301 " - " ASN A 600 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 654 " " NAG A1305 " - " ASN A1131 " " NAG A1307 " - " ASN A 231 " " NAG A1308 " - " ASN A 340 " " NAG A1309 " - " ASN A 367 " " NAG C1301 " - " ASN C 600 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG E1301 " - " ASN E 231 " " NAG E1302 " - " ASN E 61 " " NAG E1303 " - " ASN E 328 " " NAG E1304 " - " ASN E 613 " " NAG E1305 " - " ASN E 654 " " NAG E1306 " - " ASN E1071 " " NAG E1307 " - " ASN E 340 " " NAG E1308 " - " ASN E 160 " " NAG E1309 " - " ASN E 135 " " NAG I 1 " - " ASN C1095 " " NAG J 1 " - " ASN C1131 " " NAG K 1 " - " ASN C 706 " " NAG M 1 " - " ASN C 714 " " NAG N 1 " - " ASN C 798 " " NAG O 1 " - " ASN C1071 " " NAG P 1 " - " ASN C 279 " " NAG Q 1 " - " ASN A1095 " " NAG R 1 " - " ASN A 706 " " NAG S 1 " - " ASN A 714 " " NAG T 1 " - " ASN A 798 " " NAG U 1 " - " ASN A1071 " " NAG V 1 " - " ASN A 279 " " NAG W 1 " - " ASN E 120 " " NAG X 1 " - " ASN E 279 " " NAG Y 1 " - " ASN E 706 " " NAG Z 1 " - " ASN E1131 " " NAG a 1 " - " ASN E1095 " " NAG b 1 " - " ASN E 714 " " NAG c 1 " - " ASN E 798 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.4 microseconds 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7290 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 59 sheets defined 22.0% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.536A pdb=" N VAL C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.754A pdb=" N LEU C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 495 through 501 removed outlier: 3.839A pdb=" N VAL C 500 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 501 " --> pdb=" O THR C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.737A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 4.034A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.539A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.329A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 removed outlier: 3.577A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 965 removed outlier: 3.504A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.597A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU C 981 " --> pdb=" O ILE C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.859A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1142 removed outlier: 3.671A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.801A pdb=" N LEU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.533A pdb=" N ASN A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 495 through 500 removed outlier: 4.597A pdb=" N VAL A 500 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.614A pdb=" N GLY A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 824 removed outlier: 3.575A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.301A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.593A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 964 removed outlier: 4.040A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.185A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1142 removed outlier: 3.783A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.589A pdb=" N VAL E 154 " --> pdb=" O SER E 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 150 through 154' Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 361 through 368 removed outlier: 4.112A pdb=" N LEU E 365 " --> pdb=" O ASP E 361 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.616A pdb=" N LEU E 384 " --> pdb=" O PRO E 381 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN E 385 " --> pdb=" O THR E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 3.513A pdb=" N ALA E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 419 Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.948A pdb=" N GLN E 503 " --> pdb=" O GLY E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 740 removed outlier: 3.623A pdb=" N TYR E 738 " --> pdb=" O ASP E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 754 removed outlier: 3.754A pdb=" N GLY E 754 " --> pdb=" O LEU E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 780 Processing helix chain 'E' and resid 813 through 824 Processing helix chain 'E' and resid 845 through 852 Processing helix chain 'E' and resid 863 through 881 Processing helix chain 'E' and resid 883 through 888 Processing helix chain 'E' and resid 894 through 907 Processing helix chain 'E' and resid 909 through 916 removed outlier: 4.226A pdb=" N LEU E 913 " --> pdb=" O THR E 909 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR E 914 " --> pdb=" O GLN E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 937 removed outlier: 3.681A pdb=" N GLN E 932 " --> pdb=" O ILE E 928 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 933 " --> pdb=" O GLY E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 965 removed outlier: 3.629A pdb=" N LEU E 963 " --> pdb=" O LEU E 959 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 964 " --> pdb=" O VAL E 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 981 Processing helix chain 'E' and resid 982 through 1029 Processing helix chain 'E' and resid 1137 through 1142 Processing helix chain 'G' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.463A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 63 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 264 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.802A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.830A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.376A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 240 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE C 99 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.595A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 322 through 323 removed outlier: 6.889A pdb=" N ILE C 323 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE C 562 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.972A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.972A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.126A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 450 through 451 Processing sheet with id=AB3, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.529A pdb=" N TYR C 486 " --> pdb=" O TYR C 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.975A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 698 through 701 removed outlier: 3.581A pdb=" N LYS E 787 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.690A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.690A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 730 through 732 removed outlier: 4.494A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 785 through 786 removed outlier: 5.924A pdb=" N ILE C 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AC2, first strand: chain 'H' and resid 57 through 60 removed outlier: 5.928A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.508A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.430A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.290A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.304A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AC9, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.515A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 240 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 99 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.472A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.665A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 432 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.245A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 657 removed outlier: 5.880A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL A 653 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.785A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.892A pdb=" N ILE A 785 " --> pdb=" O ASN E 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AE1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AE2, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AE3, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.752A pdb=" N VAL B 114 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.713A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.415A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 30 removed outlier: 3.604A pdb=" N VAL E 88 " --> pdb=" O PHE E 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL E 224 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER E 200 " --> pdb=" O PRO E 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 48 through 55 removed outlier: 4.243A pdb=" N ASP E 284 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.333A pdb=" N GLY E 101 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ILE E 126 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR E 162 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL E 128 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN E 160 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLU E 130 " --> pdb=" O ALA E 158 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA E 158 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN E 132 " --> pdb=" O SER E 156 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 308 through 316 removed outlier: 5.554A pdb=" N ILE E 309 " --> pdb=" O THR E 596 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR E 596 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN E 311 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL E 594 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER E 313 " --> pdb=" O VAL E 592 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY E 591 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 321 through 325 removed outlier: 3.908A pdb=" N GLU E 321 " --> pdb=" O CYS E 535 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP E 571 " --> pdb=" O ILE E 584 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 351 through 354 removed outlier: 4.834A pdb=" N ASN E 391 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU E 513 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 351 through 354 Processing sheet with id=AF5, first strand: chain 'E' and resid 449 through 451 Processing sheet with id=AF6, first strand: chain 'E' and resid 651 through 653 removed outlier: 4.449A pdb=" N THR E 693 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 667 " --> pdb=" O ILE E 663 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 708 through 725 removed outlier: 6.756A pdb=" N SER E 708 " --> pdb=" O THR E1073 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR E1073 " --> pdb=" O SER E 708 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA E 710 " --> pdb=" O ASN E1071 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E1071 " --> pdb=" O ALA E 710 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU E1069 " --> pdb=" O PRO E 712 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY E1056 " --> pdb=" O SER E1052 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER E1052 " --> pdb=" O GLY E1056 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL E1058 " --> pdb=" O PRO E1050 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU E1060 " --> pdb=" O SER E1048 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER E1048 " --> pdb=" O LEU E1060 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E1062 " --> pdb=" O LEU E1046 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 708 through 725 removed outlier: 6.756A pdb=" N SER E 708 " --> pdb=" O THR E1073 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR E1073 " --> pdb=" O SER E 708 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA E 710 " --> pdb=" O ASN E1071 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E1071 " --> pdb=" O ALA E 710 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU E1069 " --> pdb=" O PRO E 712 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E1075 " --> pdb=" O PHE E1092 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE E1092 " --> pdb=" O ALA E1075 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 730 through 733 removed outlier: 4.389A pdb=" N LYS E 730 " --> pdb=" O LEU E 858 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 1117 through 1122 removed outlier: 4.291A pdb=" N ALA E1084 " --> pdb=" O SER E1120 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.230A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 86 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.612A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3213 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: 9.28 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9947 1.35 - 1.47: 8137 1.47 - 1.59: 13937 1.59 - 1.71: 2 1.71 - 1.83: 177 Bond restraints: 32200 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG E1306 " pdb=" O5 NAG E1306 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 32195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 43151 2.48 - 4.95: 554 4.95 - 7.43: 63 7.43 - 9.91: 4 9.91 - 12.38: 2 Bond angle restraints: 43774 Sorted by residual: angle pdb=" C GLY A 479 " pdb=" N VAL A 480 " pdb=" CA VAL A 480 " ideal model delta sigma weight residual 121.97 129.57 -7.60 1.80e+00 3.09e-01 1.78e+01 angle pdb=" C ASN E 85 " pdb=" CA ASN E 85 " pdb=" CB ASN E 85 " ideal model delta sigma weight residual 115.89 110.53 5.36 1.32e+00 5.74e-01 1.65e+01 angle pdb=" CA PRO L 96 " pdb=" N PRO L 96 " pdb=" CD PRO L 96 " ideal model delta sigma weight residual 112.00 106.88 5.12 1.40e+00 5.10e-01 1.34e+01 angle pdb=" CA MET C 737 " pdb=" CB MET C 737 " pdb=" CG MET C 737 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA LEU C 422 " pdb=" CB LEU C 422 " pdb=" CG LEU C 422 " ideal model delta sigma weight residual 116.30 128.68 -12.38 3.50e+00 8.16e-02 1.25e+01 ... (remaining 43769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 17798 24.95 - 49.89: 1682 49.89 - 74.84: 312 74.84 - 99.78: 131 99.78 - 124.73: 88 Dihedral angle restraints: 20011 sinusoidal: 8653 harmonic: 11358 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 5.88 87.12 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS A 837 " pdb=" SG CYS A 837 " pdb=" SG CYS A 848 " pdb=" CB CYS A 848 " ideal model delta sinusoidal sigma weight residual -86.00 -169.27 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CA SER L 95 " pdb=" C SER L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 20008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 5008 0.128 - 0.256: 46 0.256 - 0.384: 12 0.384 - 0.512: 4 0.512 - 0.640: 1 Chirality restraints: 5071 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C1095 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 600 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 5068 not shown) Planarity restraints: 5607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 95 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO F 96 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO F 96 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 96 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " 0.084 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO L 96 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 95 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO D 96 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO D 96 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 96 " -0.063 5.00e-02 4.00e+02 ... (remaining 5604 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 777 2.67 - 3.22: 32294 3.22 - 3.78: 55179 3.78 - 4.34: 73829 4.34 - 4.90: 113978 Nonbonded interactions: 276057 Sorted by model distance: nonbonded pdb=" OH TYR E 652 " pdb=" OG1 THR E 693 " model vdw 2.107 3.040 nonbonded pdb=" O ALA E 289 " pdb=" OG1 THR E 629 " model vdw 2.117 3.040 nonbonded pdb=" OG SER C 491 " pdb=" OG SER C 493 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR A 107 " pdb=" OD2 ASP A 109 " model vdw 2.143 3.040 nonbonded pdb=" OG SER G 17 " pdb=" OE1 GLN G 82 " model vdw 2.147 3.040 ... (remaining 276052 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 69 or resid 74 through 142 or resid 149 through \ 174 or resid 180 through 826 or resid 831 through 833 or (resid 834 and (name N \ or name CA or name C or name O or name CB )) or resid 835 through 837 or resid \ 845 through 1305)) selection = (chain 'C' and (resid 25 through 142 or resid 149 through 174 or resid 180 throu \ gh 244 or resid 254 through 621 or resid 629 through 826 or resid 831 through 83 \ 3 or (resid 834 and (name N or name CA or name C or name O or name CB )) or resi \ d 835 through 837 or resid 845 through 1305)) selection = (chain 'E' and (resid 25 through 174 or resid 180 through 244 or resid 254 throu \ gh 621 or resid 629 through 837 or resid 845 through 1305)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' 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: 2.240 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.190 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 32309 Z= 0.190 Angle : 0.738 16.192 44053 Z= 0.372 Chirality : 0.050 0.640 5071 Planarity : 0.006 0.127 5566 Dihedral : 21.878 124.730 12577 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Rotamer: Outliers : 0.38 % Allowed : 32.27 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: 0.05 (0.13), residues: 3850 helix: 2.30 (0.19), residues: 706 sheet: -0.01 (0.17), residues: 830 loop : -0.67 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 270 TYR 0.026 0.001 TYR C 492 PHE 0.031 0.001 PHE E 562 TRP 0.022 0.002 TRP H 47 HIS 0.003 0.001 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00389 (32200) covalent geometry : angle 0.69679 (43774) SS BOND : bond 0.00279 ( 48) SS BOND : angle 0.97491 ( 96) hydrogen bonds : bond 0.26402 ( 1138) hydrogen bonds : angle 9.69915 ( 3213) link_BETA1-4 : bond 0.00828 ( 20) link_BETA1-4 : angle 2.54931 ( 60) link_NAG-ASN : bond 0.00929 ( 41) link_NAG-ASN : angle 4.28576 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 113 MET cc_start: 0.9696 (tpt) cc_final: 0.9265 (mmm) REVERT: A 897 MET cc_start: 0.8859 (mmm) cc_final: 0.8387 (mmt) REVERT: E 368 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7267 (mt) REVERT: E 866 MET cc_start: 0.9296 (ptp) cc_final: 0.9094 (ptp) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.2182 time to fit residues: 21.3087 Evaluate side-chains 49 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 288 CYS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 1040 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN C 202 HIS ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN C 502 HIS ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN C 610 GLN C 700 ASN C 850 GLN C 989 GLN C1020 ASN C1098 HIS C1103 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 434 ASN A 436 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 638 ASN A 954 GLN A 989 GLN A1055 HIS ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 GLN E 367 ASN E 391 ASN E 484 ASN E 503 GLN ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 748 ASN E 759 GLN ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN E1008 GLN ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.024476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.018187 restraints weight = 548339.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.018657 restraints weight = 328555.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.018969 restraints weight = 230270.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.019127 restraints weight = 180714.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.019258 restraints weight = 157772.517| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 32309 Z= 0.257 Angle : 0.764 14.697 44053 Z= 0.377 Chirality : 0.050 0.430 5071 Planarity : 0.006 0.125 5566 Dihedral : 16.973 101.874 5557 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.58 % Favored : 96.23 % Rotamer: Outliers : 4.83 % Allowed : 28.97 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: 0.03 (0.13), residues: 3850 helix: 2.30 (0.19), residues: 735 sheet: -0.16 (0.17), residues: 854 loop : -0.68 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 270 TYR 0.020 0.002 TYR A 362 PHE 0.014 0.002 PHE G 105 TRP 0.021 0.002 TRP C 64 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00536 (32200) covalent geometry : angle 0.73018 (43774) SS BOND : bond 0.00402 ( 48) SS BOND : angle 1.14567 ( 96) hydrogen bonds : bond 0.05959 ( 1138) hydrogen bonds : angle 7.38332 ( 3213) link_BETA1-4 : bond 0.00771 ( 20) link_BETA1-4 : angle 2.21760 ( 60) link_NAG-ASN : bond 0.00783 ( 41) link_NAG-ASN : angle 4.00319 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 42 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8150 (tptp) REVERT: C 263 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8405 (m-80) REVERT: A 436 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8739 (m-40) REVERT: A 869 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8730 (mp10) REVERT: A 909 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.9032 (p) REVERT: A 989 GLN cc_start: 0.9702 (OUTLIER) cc_final: 0.9209 (mm-40) REVERT: E 368 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7368 (mt) REVERT: E 453 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7920 (m-80) outliers start: 164 outliers final: 78 residues processed: 199 average time/residue: 0.1942 time to fit residues: 65.8212 Evaluate side-chains 127 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 41 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 288 CYS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1133 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 211 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 337 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 335 optimal weight: 30.0000 chunk 341 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN C 414 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN C 916 ASN C1103 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 748 ASN A 784 GLN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 917 GLN ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1033 GLN ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.024538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.018232 restraints weight = 539918.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.018717 restraints weight = 322636.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.019037 restraints weight = 225711.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.019194 restraints weight = 176969.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.019334 restraints weight = 155466.315| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 32309 Z= 0.158 Angle : 0.713 14.064 44053 Z= 0.343 Chirality : 0.050 0.846 5071 Planarity : 0.006 0.126 5566 Dihedral : 14.716 97.696 5553 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.43 % Favored : 96.39 % Rotamer: Outliers : 4.19 % Allowed : 29.30 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.02 (0.13), residues: 3850 helix: 2.25 (0.19), residues: 741 sheet: -0.29 (0.17), residues: 880 loop : -0.67 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 270 TYR 0.019 0.001 TYR H 52 PHE 0.015 0.001 PHE C 181 TRP 0.013 0.001 TRP C 64 HIS 0.007 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00340 (32200) covalent geometry : angle 0.67402 (43774) SS BOND : bond 0.00334 ( 48) SS BOND : angle 1.06022 ( 96) hydrogen bonds : bond 0.05021 ( 1138) hydrogen bonds : angle 6.84074 ( 3213) link_BETA1-4 : bond 0.00787 ( 20) link_BETA1-4 : angle 2.34448 ( 60) link_NAG-ASN : bond 0.00760 ( 41) link_NAG-ASN : angle 4.10806 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 41 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8132 (tptp) REVERT: C 836 ASP cc_start: 0.2424 (OUTLIER) cc_final: 0.2207 (m-30) REVERT: C 902 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.7980 (mmt90) REVERT: A 469 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8396 (pt) REVERT: A 909 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9016 (p) REVERT: A 1110 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8652 (mm-40) REVERT: E 277 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8655 (p0) REVERT: E 453 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: E 1026 MET cc_start: 0.9701 (tpt) cc_final: 0.9399 (tpt) outliers start: 142 outliers final: 78 residues processed: 179 average time/residue: 0.1704 time to fit residues: 52.1355 Evaluate side-chains 127 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 41 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 902 ARG Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 288 CYS Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 109 optimal weight: 0.9990 chunk 297 optimal weight: 7.9990 chunk 354 optimal weight: 9.9990 chunk 114 optimal weight: 30.0000 chunk 276 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 123 optimal weight: 40.0000 chunk 239 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 436 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 GLN A1103 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.3272 r_free = 0.3272 target = 0.024423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.018107 restraints weight = 541731.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.018582 restraints weight = 320873.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.018895 restraints weight = 225067.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.019054 restraints weight = 177054.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.019197 restraints weight = 154973.840| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 32309 Z= 0.182 Angle : 0.699 13.902 44053 Z= 0.336 Chirality : 0.047 0.332 5071 Planarity : 0.006 0.126 5566 Dihedral : 12.734 95.128 5551 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.90 % Favored : 95.90 % Rotamer: Outliers : 5.13 % Allowed : 28.32 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.07 (0.13), residues: 3850 helix: 2.22 (0.19), residues: 749 sheet: -0.43 (0.17), residues: 889 loop : -0.67 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 405 TYR 0.018 0.001 TYR C 450 PHE 0.013 0.001 PHE G 105 TRP 0.024 0.001 TRP B 33 HIS 0.005 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00388 (32200) covalent geometry : angle 0.66114 (43774) SS BOND : bond 0.00374 ( 48) SS BOND : angle 1.08690 ( 96) hydrogen bonds : bond 0.04535 ( 1138) hydrogen bonds : angle 6.54913 ( 3213) link_BETA1-4 : bond 0.00839 ( 20) link_BETA1-4 : angle 2.56468 ( 60) link_NAG-ASN : bond 0.01087 ( 41) link_NAG-ASN : angle 3.90067 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 41 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8139 (tptp) REVERT: C 836 ASP cc_start: 0.2760 (OUTLIER) cc_final: 0.2543 (m-30) REVERT: A 436 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8883 (m-40) REVERT: A 469 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (pt) REVERT: A 866 MET cc_start: 0.9345 (pmm) cc_final: 0.8973 (pmm) REVERT: A 909 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9008 (p) REVERT: A 1110 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8604 (mm-40) REVERT: E 368 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7268 (mt) REVERT: E 453 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: E 897 MET cc_start: 0.9112 (mtp) cc_final: 0.8882 (mtt) REVERT: E 915 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8090 (mt-10) outliers start: 174 outliers final: 128 residues processed: 211 average time/residue: 0.1956 time to fit residues: 68.5214 Evaluate side-chains 178 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 41 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 902 ARG Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1095 ASN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 288 CYS Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 562 PHE Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 370 optimal weight: 20.0000 chunk 284 optimal weight: 3.9990 chunk 116 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 231 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 99 optimal weight: 0.0870 chunk 12 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 overall best weight: 4.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 436 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 ASN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 951 HIS ** E 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.024425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.018063 restraints weight = 547231.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.018547 restraints weight = 315560.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.018859 restraints weight = 219810.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.019028 restraints weight = 172506.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.019178 restraints weight = 149951.925| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 32309 Z= 0.164 Angle : 0.682 13.595 44053 Z= 0.328 Chirality : 0.046 0.330 5071 Planarity : 0.005 0.125 5566 Dihedral : 11.543 96.756 5550 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.82 % Favored : 95.97 % Rotamer: Outliers : 5.36 % Allowed : 28.18 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.10 (0.13), residues: 3850 helix: 2.27 (0.19), residues: 745 sheet: -0.45 (0.17), residues: 903 loop : -0.71 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 316 TYR 0.017 0.001 TYR B 52 PHE 0.013 0.001 PHE G 105 TRP 0.017 0.001 TRP C 64 HIS 0.004 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00354 (32200) covalent geometry : angle 0.64361 (43774) SS BOND : bond 0.00328 ( 48) SS BOND : angle 0.95173 ( 96) hydrogen bonds : bond 0.04336 ( 1138) hydrogen bonds : angle 6.36334 ( 3213) link_BETA1-4 : bond 0.00761 ( 20) link_BETA1-4 : angle 2.65878 ( 60) link_NAG-ASN : bond 0.00819 ( 41) link_NAG-ASN : angle 3.89289 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 41 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8183 (tptp) REVERT: H 6 GLN cc_start: 0.9440 (OUTLIER) cc_final: 0.9106 (mt0) REVERT: A 469 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8404 (pt) REVERT: A 737 MET cc_start: 0.9414 (ppp) cc_final: 0.9192 (ppp) REVERT: A 866 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8916 (pmm) REVERT: A 909 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.8996 (p) REVERT: A 989 GLN cc_start: 0.9630 (OUTLIER) cc_final: 0.8757 (mm-40) REVERT: A 1110 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8649 (mm-40) REVERT: E 368 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7220 (mt) REVERT: E 385 ASN cc_start: 0.9523 (OUTLIER) cc_final: 0.8631 (m110) REVERT: E 453 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: E 897 MET cc_start: 0.9014 (mtp) cc_final: 0.8783 (mtt) REVERT: E 915 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8042 (mt-10) outliers start: 182 outliers final: 133 residues processed: 219 average time/residue: 0.1783 time to fit residues: 66.0527 Evaluate side-chains 184 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 40 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 902 ARG Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 1095 ASN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 562 PHE Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 125 optimal weight: 50.0000 chunk 301 optimal weight: 2.9990 chunk 242 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 260 optimal weight: 30.0000 chunk 339 optimal weight: 8.9990 chunk 364 optimal weight: 6.9990 chunk 256 optimal weight: 20.0000 chunk 285 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1132 ASN ** F 90 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 = 0.3263 r_free = 0.3263 target = 0.024290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.017994 restraints weight = 545919.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.018458 restraints weight = 321821.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.018755 restraints weight = 225656.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.018948 restraints weight = 177968.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.019061 restraints weight = 152492.651| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 32309 Z= 0.213 Angle : 0.690 13.623 44053 Z= 0.335 Chirality : 0.046 0.325 5071 Planarity : 0.005 0.124 5566 Dihedral : 10.742 98.781 5549 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.23 % Favored : 95.56 % Rotamer: Outliers : 5.75 % Allowed : 27.47 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.15 (0.13), residues: 3850 helix: 2.21 (0.19), residues: 751 sheet: -0.49 (0.17), residues: 914 loop : -0.74 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 185 TYR 0.022 0.001 TYR H 52 PHE 0.015 0.001 PHE E 556 TRP 0.020 0.001 TRP C 64 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00448 (32200) covalent geometry : angle 0.65390 (43774) SS BOND : bond 0.00491 ( 48) SS BOND : angle 1.17494 ( 96) hydrogen bonds : bond 0.04317 ( 1138) hydrogen bonds : angle 6.34313 ( 3213) link_BETA1-4 : bond 0.00733 ( 20) link_BETA1-4 : angle 2.63070 ( 60) link_NAG-ASN : bond 0.00780 ( 41) link_NAG-ASN : angle 3.72008 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 40 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8107 (tptp) REVERT: H 6 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.9215 (mt0) REVERT: A 469 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8510 (pt) REVERT: A 737 MET cc_start: 0.9429 (ppp) cc_final: 0.9172 (ppp) REVERT: A 866 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8924 (pmm) REVERT: A 909 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.8938 (p) REVERT: A 1110 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8627 (mm-40) REVERT: E 273 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7714 (mt) REVERT: E 368 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7234 (mt) REVERT: E 453 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: E 897 MET cc_start: 0.9122 (mtp) cc_final: 0.8869 (mtt) REVERT: E 915 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8080 (mt-10) outliers start: 195 outliers final: 148 residues processed: 232 average time/residue: 0.1837 time to fit residues: 70.9894 Evaluate side-chains 198 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 40 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 902 ARG Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1095 ASN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 562 PHE Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1062 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 286 optimal weight: 30.0000 chunk 256 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.024305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.018007 restraints weight = 549739.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.018482 restraints weight = 315422.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.018788 restraints weight = 220301.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.018976 restraints weight = 173248.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.019100 restraints weight = 148004.077| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 32309 Z= 0.186 Angle : 0.676 13.418 44053 Z= 0.328 Chirality : 0.046 0.340 5071 Planarity : 0.005 0.124 5566 Dihedral : 10.096 99.611 5549 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.31 % Favored : 95.48 % Rotamer: Outliers : 5.60 % Allowed : 27.76 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.13 (0.13), residues: 3850 helix: 2.31 (0.19), residues: 746 sheet: -0.52 (0.17), residues: 903 loop : -0.73 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 643 TYR 0.027 0.001 TYR C 492 PHE 0.018 0.001 PHE A 494 TRP 0.020 0.001 TRP C 64 HIS 0.004 0.001 HIS E1045 Details of bonding type rmsd covalent geometry : bond 0.00397 (32200) covalent geometry : angle 0.64063 (43774) SS BOND : bond 0.00353 ( 48) SS BOND : angle 1.08250 ( 96) hydrogen bonds : bond 0.04164 ( 1138) hydrogen bonds : angle 6.23293 ( 3213) link_BETA1-4 : bond 0.00740 ( 20) link_BETA1-4 : angle 2.66814 ( 60) link_NAG-ASN : bond 0.00732 ( 41) link_NAG-ASN : angle 3.62672 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 40 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8230 (tptp) REVERT: H 6 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.9129 (mt0) REVERT: A 469 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (pt) REVERT: A 737 MET cc_start: 0.9454 (ppp) cc_final: 0.9198 (ppp) REVERT: A 866 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8939 (pmm) REVERT: A 909 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8933 (p) REVERT: A 1110 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8624 (mm-40) REVERT: E 273 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7787 (mt) REVERT: E 368 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7180 (mt) REVERT: E 453 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: E 897 MET cc_start: 0.9012 (mtp) cc_final: 0.8771 (mtt) REVERT: E 915 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: G 93 MET cc_start: 0.9193 (tpp) cc_final: 0.8962 (tpp) outliers start: 190 outliers final: 154 residues processed: 225 average time/residue: 0.1798 time to fit residues: 68.3622 Evaluate side-chains 204 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 40 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 902 ARG Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1095 ASN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 562 PHE Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1062 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 349 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 254 optimal weight: 40.0000 chunk 130 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 302 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN A 49 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.3265 r_free = 0.3265 target = 0.024288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.017977 restraints weight = 541280.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.018466 restraints weight = 324836.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.018777 restraints weight = 226228.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.018927 restraints weight = 176008.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.019070 restraints weight = 153231.676| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 32309 Z= 0.154 Angle : 0.660 13.208 44053 Z= 0.321 Chirality : 0.046 0.334 5071 Planarity : 0.005 0.124 5566 Dihedral : 9.502 99.941 5549 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.13 % Favored : 95.66 % Rotamer: Outliers : 5.22 % Allowed : 27.94 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.11 (0.13), residues: 3850 helix: 2.38 (0.19), residues: 740 sheet: -0.47 (0.17), residues: 922 loop : -0.76 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 270 TYR 0.031 0.001 TYR C 492 PHE 0.015 0.001 PHE A 494 TRP 0.020 0.001 TRP C 64 HIS 0.010 0.001 HIS C 502 Details of bonding type rmsd covalent geometry : bond 0.00338 (32200) covalent geometry : angle 0.62561 (43774) SS BOND : bond 0.00306 ( 48) SS BOND : angle 1.07722 ( 96) hydrogen bonds : bond 0.03993 ( 1138) hydrogen bonds : angle 6.06573 ( 3213) link_BETA1-4 : bond 0.00782 ( 20) link_BETA1-4 : angle 2.70341 ( 60) link_NAG-ASN : bond 0.00686 ( 41) link_NAG-ASN : angle 3.47986 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 40 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8211 (tptp) REVERT: C 464 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7980 (p0) REVERT: H 6 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8828 (mt0) REVERT: L 90 GLN cc_start: 0.9497 (OUTLIER) cc_final: 0.9248 (pp30) REVERT: A 469 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8403 (pt) REVERT: A 866 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8934 (pmm) REVERT: A 909 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 1110 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8633 (mm-40) REVERT: E 273 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7756 (mt) REVERT: E 368 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7137 (mt) REVERT: E 453 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: E 897 MET cc_start: 0.8996 (mtp) cc_final: 0.8760 (mtt) REVERT: G 93 MET cc_start: 0.9227 (tpp) cc_final: 0.9021 (tpp) outliers start: 177 outliers final: 148 residues processed: 212 average time/residue: 0.1761 time to fit residues: 62.5530 Evaluate side-chains 199 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 40 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 902 ARG Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1095 ASN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 562 PHE Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1062 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 214 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 368 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 326 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 ASN ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 932 GLN ** E1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.3256 r_free = 0.3256 target = 0.024172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.017893 restraints weight = 551232.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.018372 restraints weight = 326781.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.018681 restraints weight = 227223.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.018858 restraints weight = 177293.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.018962 restraints weight = 152220.093| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 32309 Z= 0.215 Angle : 0.688 13.296 44053 Z= 0.337 Chirality : 0.046 0.358 5071 Planarity : 0.005 0.125 5566 Dihedral : 9.285 100.576 5549 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.42 % Favored : 95.40 % Rotamer: Outliers : 5.42 % Allowed : 27.97 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.14 (0.13), residues: 3850 helix: 2.33 (0.19), residues: 746 sheet: -0.55 (0.17), residues: 900 loop : -0.74 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 185 TYR 0.023 0.001 TYR C 492 PHE 0.015 0.001 PHE A 494 TRP 0.021 0.001 TRP C 64 HIS 0.004 0.001 HIS E1045 Details of bonding type rmsd covalent geometry : bond 0.00455 (32200) covalent geometry : angle 0.65454 (43774) SS BOND : bond 0.00368 ( 48) SS BOND : angle 1.45674 ( 96) hydrogen bonds : bond 0.04141 ( 1138) hydrogen bonds : angle 6.12326 ( 3213) link_BETA1-4 : bond 0.00755 ( 20) link_BETA1-4 : angle 2.71967 ( 60) link_NAG-ASN : bond 0.00711 ( 41) link_NAG-ASN : angle 3.43096 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 40 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8219 (tptp) REVERT: C 172 MET cc_start: 0.9338 (mpp) cc_final: 0.9080 (mmm) REVERT: H 6 GLN cc_start: 0.9411 (OUTLIER) cc_final: 0.9044 (mt0) REVERT: A 469 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8509 (pt) REVERT: A 866 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8943 (pmm) REVERT: A 909 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.8895 (p) REVERT: A 1110 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8645 (mm-40) REVERT: E 273 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7796 (mt) REVERT: E 368 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7141 (mt) REVERT: E 453 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: E 897 MET cc_start: 0.9018 (mtp) cc_final: 0.8770 (mtt) REVERT: E 915 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8071 (mt-10) outliers start: 184 outliers final: 155 residues processed: 220 average time/residue: 0.1845 time to fit residues: 67.6529 Evaluate side-chains 205 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 40 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 902 ARG Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1052 SER Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1095 ASN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 562 PHE Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 610 GLN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 730 LYS Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 90 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 264 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 368 optimal weight: 10.0000 chunk 269 optimal weight: 30.0000 chunk 240 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 382 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 610 GLN A 700 ASN A 910 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 752 GLN ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 946 GLN ** E1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.024159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.017836 restraints weight = 559471.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.018313 restraints weight = 325722.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.018625 restraints weight = 225207.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.018811 restraints weight = 174445.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.018921 restraints weight = 149349.934| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 32309 Z= 0.271 Angle : 0.731 13.445 44053 Z= 0.362 Chirality : 0.047 0.344 5071 Planarity : 0.006 0.124 5566 Dihedral : 9.250 101.662 5549 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.99 % Rotamer: Outliers : 5.01 % Allowed : 28.56 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.26 (0.13), residues: 3850 helix: 2.15 (0.19), residues: 749 sheet: -0.62 (0.17), residues: 906 loop : -0.79 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 643 TYR 0.023 0.002 TYR C 492 PHE 0.048 0.002 PHE A 152 TRP 0.021 0.002 TRP C 64 HIS 0.006 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00566 (32200) covalent geometry : angle 0.70015 (43774) SS BOND : bond 0.00391 ( 48) SS BOND : angle 1.45536 ( 96) hydrogen bonds : bond 0.04402 ( 1138) hydrogen bonds : angle 6.31622 ( 3213) link_BETA1-4 : bond 0.00752 ( 20) link_BETA1-4 : angle 2.74958 ( 60) link_NAG-ASN : bond 0.00798 ( 41) link_NAG-ASN : angle 3.41617 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 40 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8156 (tptp) REVERT: C 172 MET cc_start: 0.9324 (mpp) cc_final: 0.9064 (mmm) REVERT: H 6 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.9051 (mt0) REVERT: A 866 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8956 (pmm) REVERT: A 909 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.8894 (p) REVERT: A 1110 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8714 (mm-40) REVERT: E 273 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7830 (mt) REVERT: E 368 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7318 (mt) REVERT: E 453 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: E 897 MET cc_start: 0.8975 (mtp) cc_final: 0.8616 (mtt) REVERT: E 915 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: E 1026 MET cc_start: 0.9686 (tpt) cc_final: 0.9347 (tpt) REVERT: F 21 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8546 (mt) outliers start: 170 outliers final: 148 residues processed: 206 average time/residue: 0.1903 time to fit residues: 65.2169 Evaluate side-chains 198 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 40 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 1052 SER Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1095 ASN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 562 PHE Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 610 GLN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 730 LYS Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 354 optimal weight: 7.9990 chunk 157 optimal weight: 40.0000 chunk 353 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 255 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 197 optimal weight: 0.0670 chunk 95 optimal weight: 5.9990 chunk 167 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.024192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.017907 restraints weight = 560547.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.018375 restraints weight = 330065.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.018619 restraints weight = 229759.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.018843 restraints weight = 182281.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.018971 restraints weight = 155126.390| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 32309 Z= 0.249 Angle : 0.816 57.298 44053 Z= 0.450 Chirality : 0.046 0.395 5071 Planarity : 0.006 0.124 5566 Dihedral : 9.263 101.630 5549 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.99 % Rotamer: Outliers : 5.16 % Allowed : 28.29 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 aren not related in a simple way. whole: -0.27 (0.13), residues: 3850 helix: 2.15 (0.19), residues: 748 sheet: -0.63 (0.17), residues: 906 loop : -0.80 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 902 TYR 0.021 0.002 TYR C 492 PHE 0.033 0.002 PHE A 152 TRP 0.021 0.002 TRP C 64 HIS 0.059 0.002 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00531 (32200) covalent geometry : angle 0.78923 (43774) SS BOND : bond 0.00391 ( 48) SS BOND : angle 1.42517 ( 96) hydrogen bonds : bond 0.04375 ( 1138) hydrogen bonds : angle 6.30902 ( 3213) link_BETA1-4 : bond 0.00767 ( 20) link_BETA1-4 : angle 2.75001 ( 60) link_NAG-ASN : bond 0.00786 ( 41) link_NAG-ASN : angle 3.41004 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5820.70 seconds wall clock time: 102 minutes 5.20 seconds (6125.20 seconds total)