Starting phenix.real_space_refine on Fri Jun 27 12:42:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzi_27799/06_2025/8dzi_27799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzi_27799/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dzi_27799/06_2025/8dzi_27799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzi_27799/06_2025/8dzi_27799.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzi_27799/06_2025/8dzi_27799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzi_27799/06_2025/8dzi_27799.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.78, per 1000 atoms: 0.56 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: 7.91 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 4.87 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: 15.01 Time building geometry restraints manager: 9.35 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 1144 or resid 1301 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 1144 or resid 1301 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 1144 or resid 1301 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: 2.380 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: 1.140 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 72.950 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.220 ------------------------------------------------------------------------------- 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 : 18.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (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 TRP 0.022 0.002 TRP H 47 HIS 0.003 0.001 HIS E 202 PHE 0.031 0.001 PHE E 562 TYR 0.026 0.001 TYR C 492 ARG 0.007 0.001 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 41) link_NAG-ASN : angle 4.28576 ( 123) link_BETA1-4 : bond 0.00828 ( 20) link_BETA1-4 : angle 2.54931 ( 60) hydrogen bonds : bond 0.26402 ( 1138) hydrogen bonds : angle 9.69915 ( 3213) SS BOND : bond 0.00279 ( 48) SS BOND : angle 0.97491 ( 96) covalent geometry : bond 0.00389 (32200) covalent geometry : angle 0.69679 (43774) *********************** 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 : 3.460 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: 0.4270 time to fit residues: 42.1247 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 : 3.346 ------------------------------------------------------------------------------- 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 325 optimal weight: 8.9990 chunk 292 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 302 optimal weight: 0.7980 chunk 117 optimal weight: 40.0000 chunk 183 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 801 GLN ** 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** 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.024532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.018243 restraints weight = 544325.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.018706 restraints weight = 320929.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.018992 restraints weight = 226246.318| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 32309 Z= 0.237 Angle : 0.755 14.631 44053 Z= 0.372 Chirality : 0.049 0.431 5071 Planarity : 0.006 0.125 5566 Dihedral : 16.924 100.766 5557 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 4.48 % Allowed : 29.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 3850 helix: 2.28 (0.19), residues: 736 sheet: -0.15 (0.17), residues: 868 loop : -0.68 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.005 0.001 HIS C 49 PHE 0.014 0.001 PHE G 105 TYR 0.021 0.002 TYR C 492 ARG 0.008 0.001 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00766 ( 41) link_NAG-ASN : angle 4.00002 ( 123) link_BETA1-4 : bond 0.00788 ( 20) link_BETA1-4 : angle 2.23841 ( 60) hydrogen bonds : bond 0.05726 ( 1138) hydrogen bonds : angle 7.34589 ( 3213) SS BOND : bond 0.00400 ( 48) SS BOND : angle 1.12688 ( 96) covalent geometry : bond 0.00497 (32200) covalent geometry : angle 0.72093 (43774) *********************** 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 194 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 42 time to evaluate : 3.786 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: C 127 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8165 (tptp) REVERT: C 263 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: C 902 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8187 (mmt90) REVERT: A 436 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8751 (m-40) REVERT: A 869 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8773 (mp10) REVERT: A 909 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9022 (p) REVERT: E 453 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7884 (m-80) outliers start: 152 outliers final: 69 residues processed: 188 average time/residue: 0.4032 time to fit residues: 128.3161 Evaluate side-chains 117 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 41 time to evaluate : 3.862 ------------------------------------------------------------------------------- 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 263 TYR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 393 TYR 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 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 902 ARG Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1047 MET 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 A residue 45 SER Chi-restraints excluded: chain A residue 125 VAL 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 1133 THR 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 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 615 THR Chi-restraints excluded: chain E residue 742 ASP 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 352 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 282 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 379 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 247 optimal weight: 50.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 850 GLN C 916 ASN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 784 GLN A 989 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 ASN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** 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 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** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.024489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.018182 restraints weight = 543977.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.018661 restraints weight = 320073.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.018969 restraints weight = 224328.823| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32309 Z= 0.187 Angle : 0.718 14.173 44053 Z= 0.346 Chirality : 0.049 0.527 5071 Planarity : 0.006 0.125 5566 Dihedral : 14.667 96.835 5551 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.58 % Favored : 96.23 % Rotamer: Outliers : 4.77 % Allowed : 28.65 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 3850 helix: 2.26 (0.19), residues: 739 sheet: -0.31 (0.17), residues: 880 loop : -0.65 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.006 0.001 HIS E 66 PHE 0.013 0.001 PHE G 105 TYR 0.019 0.001 TYR H 52 ARG 0.006 0.001 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00965 ( 41) link_NAG-ASN : angle 4.11207 ( 123) link_BETA1-4 : bond 0.00765 ( 20) link_BETA1-4 : angle 2.32467 ( 60) hydrogen bonds : bond 0.05072 ( 1138) hydrogen bonds : angle 6.86291 ( 3213) SS BOND : bond 0.00377 ( 48) SS BOND : angle 1.06076 ( 96) covalent geometry : bond 0.00396 (32200) covalent geometry : angle 0.67896 (43774) *********************** 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 203 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 41 time to evaluate : 5.523 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: 0.8755 (OUTLIER) cc_final: 0.8087 (tptp) REVERT: C 836 ASP cc_start: 0.2507 (OUTLIER) cc_final: 0.2241 (m-30) REVERT: A 469 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8457 (pt) REVERT: A 909 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9002 (p) REVERT: A 1110 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8645 (mm-40) REVERT: E 277 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8708 (p0) REVERT: E 368 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7275 (mt) REVERT: E 385 ASN cc_start: 0.9477 (OUTLIER) cc_final: 0.8640 (m110) REVERT: E 453 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: E 915 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: E 1026 MET cc_start: 0.9718 (tpt) cc_final: 0.9420 (tpt) outliers start: 162 outliers final: 91 residues processed: 198 average time/residue: 0.5304 time to fit residues: 181.1670 Evaluate side-chains 142 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 41 time to evaluate : 6.095 ------------------------------------------------------------------------------- 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 317 VAL Chi-restraints excluded: chain C residue 330 THR 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 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 L residue 105 VAL 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 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 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 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 SER 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 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 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 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 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 343 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 43 optimal weight: 40.0000 chunk 226 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 360 optimal weight: 0.5980 overall best weight: 6.9188 ------------------------------------------------------------------------------- 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** ** 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** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 ASN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** 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 951 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.024321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.018078 restraints weight = 552004.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.018549 restraints weight = 330738.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.018829 restraints weight = 231014.681| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 32309 Z= 0.235 Angle : 0.726 14.048 44053 Z= 0.351 Chirality : 0.047 0.383 5071 Planarity : 0.006 0.125 5566 Dihedral : 12.681 95.396 5551 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.00 % Favored : 95.79 % Rotamer: Outliers : 5.81 % Allowed : 28.06 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.13), residues: 3850 helix: 2.19 (0.19), residues: 741 sheet: -0.46 (0.17), residues: 884 loop : -0.68 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 64 HIS 0.005 0.001 HIS E1045 PHE 0.014 0.001 PHE G 105 TYR 0.017 0.002 TYR A 362 ARG 0.009 0.001 ARG E 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00950 ( 41) link_NAG-ASN : angle 4.11304 ( 123) link_BETA1-4 : bond 0.00850 ( 20) link_BETA1-4 : angle 2.55848 ( 60) hydrogen bonds : bond 0.04673 ( 1138) hydrogen bonds : angle 6.68030 ( 3213) SS BOND : bond 0.00389 ( 48) SS BOND : angle 1.09461 ( 96) covalent geometry : bond 0.00493 (32200) covalent geometry : angle 0.68682 (43774) *********************** 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 238 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 41 time to evaluate : 3.571 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: 0.8753 (OUTLIER) cc_final: 0.8064 (tptp) REVERT: C 836 ASP cc_start: 0.2810 (OUTLIER) cc_final: 0.2578 (m-30) REVERT: H 6 GLN cc_start: 0.9389 (OUTLIER) cc_final: 0.8986 (mt0) REVERT: A 436 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8738 (m-40) REVERT: A 469 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8559 (pt) REVERT: A 866 MET cc_start: 0.9349 (pmm) cc_final: 0.8945 (pmm) REVERT: A 909 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.8981 (p) REVERT: A 1110 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8638 (mm-40) REVERT: E 368 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7261 (mt) REVERT: E 385 ASN cc_start: 0.9644 (OUTLIER) cc_final: 0.9259 (m110) REVERT: E 453 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: E 915 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8062 (mt-10) outliers start: 197 outliers final: 137 residues processed: 234 average time/residue: 0.4180 time to fit residues: 164.6631 Evaluate side-chains 189 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 41 time to evaluate : 4.234 ------------------------------------------------------------------------------- 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 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 365 LEU 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 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 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 836 ASP 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 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 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 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 364 VAL 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 721 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 1047 MET 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 88 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 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 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 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 24 ARG 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 43 LYS Chi-restraints excluded: chain G residue 52 TYR 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 140 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 344 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 366 optimal weight: 30.0000 chunk 242 optimal weight: 30.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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 ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN ** 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 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** 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** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.024442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.018151 restraints weight = 539912.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.018632 restraints weight = 324251.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.018930 restraints weight = 226521.387| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 32309 Z= 0.143 Angle : 0.678 13.474 44053 Z= 0.325 Chirality : 0.047 0.388 5071 Planarity : 0.005 0.125 5566 Dihedral : 11.505 97.113 5550 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.74 % Favored : 96.05 % Rotamer: Outliers : 4.69 % Allowed : 28.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 3850 helix: 2.22 (0.19), residues: 749 sheet: -0.41 (0.17), residues: 876 loop : -0.71 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 64 HIS 0.005 0.001 HIS E 66 PHE 0.013 0.001 PHE G 105 TYR 0.024 0.001 TYR H 52 ARG 0.006 0.000 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00787 ( 41) link_NAG-ASN : angle 3.97737 ( 123) link_BETA1-4 : bond 0.00791 ( 20) link_BETA1-4 : angle 2.68204 ( 60) hydrogen bonds : bond 0.04276 ( 1138) hydrogen bonds : angle 6.38520 ( 3213) SS BOND : bond 0.00329 ( 48) SS BOND : angle 0.98698 ( 96) covalent geometry : bond 0.00314 (32200) covalent geometry : angle 0.63777 (43774) *********************** 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 201 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 42 time to evaluate : 3.365 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: C 127 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8184 (tptp) REVERT: C 836 ASP cc_start: 0.2768 (OUTLIER) cc_final: 0.2566 (m-30) REVERT: A 469 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (pt) REVERT: A 737 MET cc_start: 0.9451 (ppp) cc_final: 0.9201 (ppp) REVERT: A 866 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8942 (pmm) REVERT: A 909 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.8981 (p) REVERT: A 1110 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8610 (mm-40) REVERT: B 93 MET cc_start: 0.9418 (tpp) cc_final: 0.9207 (tpp) REVERT: E 368 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7270 (mt) REVERT: E 453 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: E 897 MET cc_start: 0.9017 (mtp) cc_final: 0.8794 (mtt) outliers start: 159 outliers final: 113 residues processed: 197 average time/residue: 0.4275 time to fit residues: 138.6818 Evaluate side-chains 162 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 41 time to evaluate : 3.852 ------------------------------------------------------------------------------- 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 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 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 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 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER 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 913 LEU 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 7 SER Chi-restraints excluded: chain H residue 20 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 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 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 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 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 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 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 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 123 ASN Chi-restraints excluded: chain E residue 237 THR 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 631 ARG Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 673 THR 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 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP 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 21 LEU Chi-restraints excluded: chain F residue 66 SER 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 363 optimal weight: 6.9990 chunk 365 optimal weight: 7.9990 chunk 282 optimal weight: 8.9990 chunk 122 optimal weight: 50.0000 chunk 114 optimal weight: 40.0000 chunk 384 optimal weight: 40.0000 chunk 166 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 553 ASN ** 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** A 49 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 ASN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** 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** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.024239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.017968 restraints weight = 553143.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.018431 restraints weight = 331608.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.018748 restraints weight = 231538.224| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 32309 Z= 0.261 Angle : 0.726 13.701 44053 Z= 0.354 Chirality : 0.047 0.385 5071 Planarity : 0.006 0.124 5566 Dihedral : 10.791 99.359 5549 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.29 % Favored : 95.51 % Rotamer: Outliers : 5.75 % Allowed : 27.53 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3850 helix: 2.12 (0.19), residues: 753 sheet: -0.50 (0.17), residues: 890 loop : -0.78 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 64 HIS 0.006 0.001 HIS A 516 PHE 0.016 0.001 PHE C 196 TYR 0.016 0.002 TYR A 362 ARG 0.006 0.001 ARG E 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00845 ( 41) link_NAG-ASN : angle 3.88044 ( 123) link_BETA1-4 : bond 0.00707 ( 20) link_BETA1-4 : angle 2.62549 ( 60) hydrogen bonds : bond 0.04480 ( 1138) hydrogen bonds : angle 6.48094 ( 3213) SS BOND : bond 0.00465 ( 48) SS BOND : angle 1.29856 ( 96) covalent geometry : bond 0.00547 (32200) covalent geometry : angle 0.68886 (43774) *********************** 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 236 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 41 time to evaluate : 3.846 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: C 127 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8102 (tptp) REVERT: C 836 ASP cc_start: 0.3234 (OUTLIER) cc_final: 0.3034 (m-30) REVERT: H 6 GLN cc_start: 0.9433 (OUTLIER) cc_final: 0.9020 (mt0) REVERT: A 469 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8515 (pt) REVERT: A 866 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8932 (pmm) REVERT: A 909 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8957 (p) REVERT: A 1110 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8644 (mm-40) REVERT: E 368 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7339 (mt) REVERT: E 385 ASN cc_start: 0.9640 (OUTLIER) cc_final: 0.8947 (m110) REVERT: E 453 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: E 897 MET cc_start: 0.8975 (mtp) cc_final: 0.8729 (mtt) REVERT: E 915 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: F 2 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8697 (mp) outliers start: 195 outliers final: 146 residues processed: 232 average time/residue: 0.4810 time to fit residues: 190.5387 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 : 3.612 ------------------------------------------------------------------------------- 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 203 THR 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 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 491 SER 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 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 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 836 ASP 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 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 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR 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 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 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 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 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 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 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 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 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 52 TYR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 285 optimal weight: 7.9990 chunk 14 optimal weight: 0.0970 chunk 305 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 281 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 203 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 302 optimal weight: 20.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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 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 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 503 GLN ** 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** ** 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 = 0.3264 r_free = 0.3264 target = 0.024317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.018047 restraints weight = 547287.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.018529 restraints weight = 323783.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.018827 restraints weight = 226988.113| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2402 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= 0.167 Angle : 0.680 13.343 44053 Z= 0.330 Chirality : 0.047 0.376 5071 Planarity : 0.005 0.124 5566 Dihedral : 10.130 99.793 5549 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.95 % Favored : 95.84 % Rotamer: Outliers : 5.28 % Allowed : 28.06 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 3850 helix: 2.24 (0.19), residues: 746 sheet: -0.55 (0.17), residues: 911 loop : -0.77 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 64 HIS 0.005 0.001 HIS C 502 PHE 0.016 0.001 PHE A 494 TYR 0.024 0.001 TYR C 492 ARG 0.006 0.000 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 41) link_NAG-ASN : angle 3.75811 ( 123) link_BETA1-4 : bond 0.00754 ( 20) link_BETA1-4 : angle 2.66163 ( 60) hydrogen bonds : bond 0.04166 ( 1138) hydrogen bonds : angle 6.30480 ( 3213) SS BOND : bond 0.00356 ( 48) SS BOND : angle 1.36695 ( 96) covalent geometry : bond 0.00362 (32200) covalent geometry : angle 0.64153 (43774) *********************** 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 219 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 40 time to evaluate : 3.736 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: 0.8782 (OUTLIER) cc_final: 0.8220 (tptp) REVERT: H 6 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9097 (mt0) REVERT: A 469 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8490 (pt) REVERT: A 737 MET cc_start: 0.9381 (ppp) cc_final: 0.9160 (ppp) REVERT: A 866 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.8949 (pmm) REVERT: A 909 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8936 (p) REVERT: A 1026 MET cc_start: 0.9396 (tpp) cc_final: 0.9127 (tpp) REVERT: A 1110 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8645 (mm-40) REVERT: E 273 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7940 (mt) REVERT: E 368 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7252 (mt) REVERT: E 453 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: E 694 MET cc_start: 0.8801 (mmm) cc_final: 0.8426 (tpt) REVERT: E 897 MET cc_start: 0.8933 (mtp) cc_final: 0.8704 (mtt) REVERT: G 93 MET cc_start: 0.9175 (tpp) cc_final: 0.8943 (tpp) outliers start: 179 outliers final: 150 residues processed: 215 average time/residue: 0.5301 time to fit residues: 192.5593 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 : 5.336 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 274 LEU 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 477 CYS 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 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 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 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 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR 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 51 THR Chi-restraints excluded: chain A residue 64 TRP 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 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 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 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 99 ILE 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 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 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 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 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 183 optimal weight: 7.9990 chunk 328 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 365 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 323 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 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 49 HIS ** 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 385 ASN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** 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 ** 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 = 0.3254 r_free = 0.3254 target = 0.024175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.017919 restraints weight = 554242.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.018375 restraints weight = 331330.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.018674 restraints weight = 234562.105| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 32309 Z= 0.233 Angle : 0.704 13.494 44053 Z= 0.344 Chirality : 0.047 0.373 5071 Planarity : 0.005 0.124 5566 Dihedral : 9.796 100.554 5549 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.36 % Favored : 95.43 % Rotamer: Outliers : 5.60 % Allowed : 27.70 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3850 helix: 2.23 (0.19), residues: 746 sheet: -0.54 (0.17), residues: 885 loop : -0.79 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.026 0.002 HIS C 516 PHE 0.013 0.001 PHE A 494 TYR 0.028 0.001 TYR C 492 ARG 0.006 0.001 ARG E 643 Details of bonding type rmsd link_NAG-ASN : bond 0.00759 ( 41) link_NAG-ASN : angle 3.67870 ( 123) link_BETA1-4 : bond 0.00744 ( 20) link_BETA1-4 : angle 2.64754 ( 60) hydrogen bonds : bond 0.04263 ( 1138) hydrogen bonds : angle 6.32580 ( 3213) SS BOND : bond 0.00372 ( 48) SS BOND : angle 1.23506 ( 96) covalent geometry : bond 0.00490 (32200) covalent geometry : angle 0.66909 (43774) *********************** 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 230 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 40 time to evaluate : 3.421 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: C 127 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8156 (tptp) REVERT: C 172 MET cc_start: 0.9257 (mpp) cc_final: 0.8967 (mmm) REVERT: C 464 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7995 (p0) REVERT: H 6 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8665 (mt0) REVERT: A 469 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8376 (pt) REVERT: A 866 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8874 (pmm) REVERT: A 909 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8911 (p) REVERT: A 1110 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8619 (mm-40) REVERT: E 273 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8106 (mt) REVERT: E 385 ASN cc_start: 0.9505 (OUTLIER) cc_final: 0.8702 (m110) REVERT: E 453 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: E 694 MET cc_start: 0.8612 (mmm) cc_final: 0.8275 (tpt) REVERT: G 40 MET cc_start: 0.9139 (mmm) cc_final: 0.8818 (mmm) outliers start: 190 outliers final: 165 residues processed: 224 average time/residue: 0.4158 time to fit residues: 157.4452 Evaluate side-chains 215 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 40 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER 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 203 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 274 LEU 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 464 ASP Chi-restraints excluded: chain C residue 477 CYS 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 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 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 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 7 SER 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 H residue 113 MET 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 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 342 THR 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 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 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 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 46 SER 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 190 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 320 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 314 optimal weight: 6.9990 chunk 364 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 122 optimal weight: 40.0000 chunk 202 optimal weight: 0.4980 chunk 315 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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** ** 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** ** A 541 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 503 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.024290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.017949 restraints weight = 551242.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.018449 restraints weight = 321372.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.018773 restraints weight = 220569.296| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 32309 Z= 0.155 Angle : 0.674 13.280 44053 Z= 0.328 Chirality : 0.047 0.364 5071 Planarity : 0.005 0.125 5566 Dihedral : 9.435 100.347 5549 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 4.98 % Allowed : 28.35 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 3850 helix: 2.32 (0.19), residues: 746 sheet: -0.57 (0.17), residues: 911 loop : -0.76 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 64 HIS 0.003 0.001 HIS E 141 PHE 0.022 0.001 PHE E 426 TYR 0.031 0.001 TYR C 492 ARG 0.006 0.000 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00693 ( 41) link_NAG-ASN : angle 3.56846 ( 123) link_BETA1-4 : bond 0.00787 ( 20) link_BETA1-4 : angle 2.71073 ( 60) hydrogen bonds : bond 0.04019 ( 1138) hydrogen bonds : angle 6.15001 ( 3213) SS BOND : bond 0.00314 ( 48) SS BOND : angle 1.49843 ( 96) covalent geometry : bond 0.00340 (32200) covalent geometry : angle 0.63700 (43774) *********************** 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 209 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 40 time to evaluate : 3.653 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: 0.8745 (OUTLIER) cc_final: 0.8204 (tptp) REVERT: C 172 MET cc_start: 0.9400 (mpp) cc_final: 0.8974 (mmm) REVERT: C 694 MET cc_start: 0.8888 (ptm) cc_final: 0.8196 (mtp) REVERT: H 6 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8913 (mt0) REVERT: A 469 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8482 (pt) REVERT: A 866 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8984 (pmm) REVERT: A 909 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.8882 (p) REVERT: A 1110 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8653 (mm-40) REVERT: E 273 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7946 (mt) REVERT: E 385 ASN cc_start: 0.9658 (OUTLIER) cc_final: 0.9081 (m110) REVERT: E 453 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: E 694 MET cc_start: 0.8851 (mmm) cc_final: 0.8531 (tpt) REVERT: E 1026 MET cc_start: 0.9680 (tpt) cc_final: 0.9291 (tpt) REVERT: F 2 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8706 (mp) outliers start: 169 outliers final: 153 residues processed: 205 average time/residue: 0.4100 time to fit residues: 141.1224 Evaluate side-chains 203 residues out of total 3406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 40 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER 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 203 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 274 LEU 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 477 CYS 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 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 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 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 112 THR 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 51 THR 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 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 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 720 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 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 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 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 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 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 730 LYS 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 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 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 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 114 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 197 optimal weight: 0.0980 chunk 364 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 165 optimal weight: 0.0270 chunk 125 optimal weight: 7.9990 chunk 344 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 53 optimal weight: 40.0000 overall best weight: 3.8244 ------------------------------------------------------------------------------- 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 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** ** 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 385 ASN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** 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 = 0.3263 r_free = 0.3263 target = 0.024229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.017942 restraints weight = 549229.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.018429 restraints weight = 327217.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.018734 restraints weight = 226472.023| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2721 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= 0.155 Angle : 0.663 13.102 44053 Z= 0.322 Chirality : 0.046 0.361 5071 Planarity : 0.005 0.125 5566 Dihedral : 9.081 100.536 5549 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.84 % Favored : 95.95 % Rotamer: Outliers : 5.01 % Allowed : 28.23 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 3850 helix: 2.36 (0.19), residues: 745 sheet: -0.55 (0.17), residues: 921 loop : -0.76 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 64 HIS 0.004 0.001 HIS E1045 PHE 0.013 0.001 PHE A 131 TYR 0.026 0.001 TYR C 492 ARG 0.010 0.000 ARG D 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 41) link_NAG-ASN : angle 3.48584 ( 123) link_BETA1-4 : bond 0.00790 ( 20) link_BETA1-4 : angle 2.75772 ( 60) hydrogen bonds : bond 0.03949 ( 1138) hydrogen bonds : angle 6.03840 ( 3213) SS BOND : bond 0.00312 ( 48) SS BOND : angle 1.27701 ( 96) covalent geometry : bond 0.00340 (32200) covalent geometry : angle 0.62801 (43774) ********************** 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 : 4.497 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: C 127 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8250 (tptp) REVERT: C 172 MET cc_start: 0.9389 (mpp) cc_final: 0.9034 (mmm) REVERT: C 464 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7955 (p0) REVERT: C 694 MET cc_start: 0.8865 (ptm) cc_final: 0.8169 (mtp) REVERT: H 6 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8883 (mt0) REVERT: A 469 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8489 (pt) REVERT: A 866 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8953 (pmm) REVERT: A 909 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8869 (p) REVERT: A 1110 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8626 (mm-40) REVERT: E 273 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7945 (mt) REVERT: E 385 ASN cc_start: 0.9631 (OUTLIER) cc_final: 0.9173 (m110) REVERT: E 453 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: E 694 MET cc_start: 0.8917 (mmm) cc_final: 0.8676 (tpt) REVERT: E 1026 MET cc_start: 0.9682 (tpt) cc_final: 0.9299 (tpt) REVERT: F 2 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 170 outliers final: 147 residues processed: 204 average time/residue: 0.5808 time to fit residues: 204.8546 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 : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 63 THR 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 203 THR Chi-restraints excluded: chain C residue 237 THR 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 347 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 477 CYS 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 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 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 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 51 ILE Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 MET 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 51 THR 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 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 342 THR 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 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 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 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 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 342 THR 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 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 730 LYS 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 291 optimal weight: 5.9990 chunk 115 optimal weight: 50.0000 chunk 286 optimal weight: 40.0000 chunk 295 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- 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 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** ** 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 385 ASN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.024154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.017894 restraints weight = 548593.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.018356 restraints weight = 329539.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.018646 restraints weight = 230592.635| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2841 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= 0.216 Angle : 0.684 13.262 44053 Z= 0.335 Chirality : 0.046 0.363 5071 Planarity : 0.005 0.124 5566 Dihedral : 8.989 101.073 5549 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.13 % Favored : 95.66 % Rotamer: Outliers : 4.98 % Allowed : 28.32 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3850 helix: 2.31 (0.19), residues: 748 sheet: -0.54 (0.17), residues: 914 loop : -0.76 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.004 0.001 HIS A 516 PHE 0.013 0.001 PHE A 32 TYR 0.025 0.001 TYR C 492 ARG 0.008 0.001 ARG D 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 41) link_NAG-ASN : angle 3.47688 ( 123) link_BETA1-4 : bond 0.00764 ( 20) link_BETA1-4 : angle 2.78088 ( 60) hydrogen bonds : bond 0.04085 ( 1138) hydrogen bonds : angle 6.11196 ( 3213) SS BOND : bond 0.00340 ( 48) SS BOND : angle 1.27476 ( 96) covalent geometry : bond 0.00458 (32200) covalent geometry : angle 0.65022 (43774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11740.79 seconds wall clock time: 213 minutes 7.00 seconds (12787.00 seconds total)