Starting phenix.real_space_refine on Fri Mar 6 05:39:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xey_22156/03_2026/6xey_22156.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xey_22156/03_2026/6xey_22156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xey_22156/03_2026/6xey_22156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xey_22156/03_2026/6xey_22156.map" model { file = "/net/cci-nas-00/data/ceres_data/6xey_22156/03_2026/6xey_22156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xey_22156/03_2026/6xey_22156.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.026 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 135 5.16 5 C 18106 2.51 5 N 4672 2.21 5 O 5569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28482 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7663 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 982} Chain breaks: 6 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 490 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 9, 'ASN:plan1': 9, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 9, 'TYR:plan': 5, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 210 Chain: "B" Number of atoms: 7630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7630 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 982} Chain breaks: 6 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 15, 'HIS:plan': 2, 'GLU:plan': 14, 'PHE:plan': 2, 'GLN:plan1': 9, 'ASN:plan1': 9, 'ARG:plan': 9, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 252 Chain: "C" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7683 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Chain breaks: 6 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 10, 'ASN:plan1': 10, 'GLU:plan': 11, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 208 Chain: "F" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 850 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 698 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 857 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 848 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "K" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 692 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 694 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.44, per 1000 atoms: 0.23 Number of scatterers: 28482 At special positions: 0 Unit cell: (148.12, 140.714, 197.846, 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 135 16.00 O 5569 8.00 N 4672 7.00 C 18106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " BMA 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-ASN " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A 801 " " NAG A1314 " - " ASN A 709 " " NAG A1315 " - " ASN A 657 " " NAG A1316 " - " ASN A 616 " " NAG A1317 " - " ASN A 603 " " NAG A1318 " - " ASN A 331 " " NAG A1319 " - " ASN A 165 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1306 " - " ASN B 331 " " NAG B1312 " - " ASN B1134 " " NAG B1313 " - " ASN B 234 " " NAG B1314 " - " ASN B 709 " " NAG B1315 " - " ASN B 165 " " NAG B1316 " - " ASN B1098 " " NAG B1317 " - " ASN B 801 " " NAG B1318 " - " ASN B1074 " " NAG B1319 " - " ASN B 616 " " NAG C1301 " - " ASN C 657 " " NAG C1305 " - " ASN C 331 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C1098 " " NAG C1315 " - " ASN C 165 " " NAG C1316 " - " ASN C 616 " " NAG C1317 " - " ASN C 709 " " NAG C1318 " - " ASN C 801 " " NAG C1319 " - " ASN C 282 " " NAG D 1 " - " ASN A 481 " " NAG E 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG M 1 " - " ASN B 481 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 481 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN F 58 " " NAG T 1 " - " ASN H 58 " " NAG U 1 " - " ASN J 58 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7018 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 64 sheets defined 20.9% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.819A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.674A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.568A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.900A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.822A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.787A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.643A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.012A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.714A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.703A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.739A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 4.330A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.567A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.632A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.503A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.762A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.731A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.595A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 removed outlier: 3.574A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 4.655A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.518A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.767A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.770A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.321A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.510A pdb=" N ASP C 571 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 568 through 572' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 749 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.270A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.680A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.681A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.079A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.274A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.719A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.172A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.666A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.952A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.816A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.767A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.837A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.710A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.116A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.951A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.939A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.696A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 319 removed outlier: 5.424A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.521A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.308A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.976A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.978A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.644A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.644A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.049A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.237A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.559A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.851A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.755A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.539A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.631A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.633A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.145A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 728 removed outlier: 6.185A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B1049 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.328A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.806A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.865A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 65 through 66 removed outlier: 4.045A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.803A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.381A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.214A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.613A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.695A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.803A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.215A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.897A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.717A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.717A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.638A pdb=" N ALA G 11 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 18 through 24 removed outlier: 3.587A pdb=" N SER G 65 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER G 63 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.615A pdb=" N SER G 90 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL G 97 " --> pdb=" O SER G 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN H 58 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AG4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.817A pdb=" N MET J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.603A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.607A pdb=" N SER K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 89 through 90 removed outlier: 3.511A pdb=" N SER K 90 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL K 97 " --> pdb=" O SER K 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.711A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.505A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.637A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 2928 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.95 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9118 1.34 - 1.46: 7559 1.46 - 1.59: 12289 1.59 - 1.71: 0 1.71 - 1.83: 178 Bond restraints: 29144 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.78e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" C1 BMA M 2 " pdb=" C2 BMA M 2 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" CB THR C1077 " pdb=" CG2 THR C1077 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 ... (remaining 29139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 38980 2.43 - 4.86: 831 4.86 - 7.29: 70 7.29 - 9.72: 15 9.72 - 12.16: 2 Bond angle restraints: 39898 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 111.36 104.35 7.01 1.09e+00 8.42e-01 4.13e+01 angle pdb=" N VAL G 51 " pdb=" CA VAL G 51 " pdb=" C VAL G 51 " ideal model delta sigma weight residual 109.34 121.50 -12.16 2.08e+00 2.31e-01 3.42e+01 angle pdb=" N GLY F 44 " pdb=" CA GLY F 44 " pdb=" C GLY F 44 " ideal model delta sigma weight residual 111.78 121.04 -9.26 1.69e+00 3.50e-01 3.00e+01 angle pdb=" N ILE B 805 " pdb=" CA ILE B 805 " pdb=" C ILE B 805 " ideal model delta sigma weight residual 111.90 107.77 4.13 8.10e-01 1.52e+00 2.60e+01 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 113.79 108.32 5.47 1.17e+00 7.31e-01 2.19e+01 ... (remaining 39893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 16888 22.34 - 44.68: 720 44.68 - 67.02: 122 67.02 - 89.37: 64 89.37 - 111.71: 20 Dihedral angle restraints: 17814 sinusoidal: 6859 harmonic: 10955 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 14.65 78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -143.39 57.39 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 147.27 -54.27 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 17811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4623 0.116 - 0.231: 140 0.231 - 0.347: 16 0.347 - 0.462: 3 0.462 - 0.578: 1 Chirality restraints: 4783 Sorted by residual: chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.34e+00 chirality pdb=" CA ASN K 31 " pdb=" N ASN K 31 " pdb=" C ASN K 31 " pdb=" CB ASN K 31 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 4780 not shown) Planarity restraints: 5166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 486 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C PHE A 486 " 0.068 2.00e-02 2.50e+03 pdb=" O PHE A 486 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 487 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1041 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ASP A1041 " 0.063 2.00e-02 2.50e+03 pdb=" O ASP A1041 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A1042 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 295 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.040 5.00e-02 4.00e+02 ... (remaining 5163 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 7402 2.79 - 3.32: 25356 3.32 - 3.85: 46652 3.85 - 4.37: 52415 4.37 - 4.90: 92148 Nonbonded interactions: 223973 Sorted by model distance: nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR L 26 " pdb=" O SER L 27A" model vdw 2.280 3.040 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR B 351 " pdb=" O ILE B 468 " model vdw 2.310 3.040 nonbonded pdb=" OG SER K 34 " pdb=" OG SER K 89 " model vdw 2.319 3.040 ... (remaining 223968 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 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 51 or (resid 52 throu \ gh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 throu \ gh 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) or r \ esid 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or \ resid 81 through 86 or (resid 87 and (name N or name CA or name C or name O or \ name CB )) or resid 88 through 94 or (resid 95 through 98 and (name N or name CA \ or name C or name O or name CB )) or resid 99 through 114 or (resid 115 and (na \ me N or name CA or name C or name O or name CB )) or resid 116 through 123 or (r \ esid 124 and (name N or name CA or name C or name O or name CB )) or resid 125 t \ hrough 133 or (resid 134 and (name N or name CA or name C or name O or name CB ) \ ) or resid 135 or (resid 136 through 138 and (name N or name CA or name C or nam \ e O or name CB )) or resid 139 through 143 or resid 158 through 160 or (resid 16 \ 1 through 164 and (name N or name CA or name C or name O or name CB )) or resid \ 165 through 205 or (resid 206 and (name N or name CA or name C or name O or name \ CB )) or resid 207 through 244 or (resid 245 through 246 and (name N or name CA \ or name C or name O or name CB )) or resid 247 through 253 or (resid 254 and (n \ ame N or name CA or name C or name O or name CB )) or resid 255 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 286 or (resid 287 through 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 through 308 or (resid 309 through 310 and (name N or \ name CA or name C or name O or name CB )) or resid 311 through 323 or (resid 32 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 325 through \ 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) or re \ sid 333 through 345 or (resid 346 and (name N or name CA or name C or name O or \ name CB )) or resid 347 through 355 or (resid 356 through 357 and (name N or nam \ e CA or name C or name O or name CB )) or resid 358 through 385 or (resid 386 an \ d (name N or name CA or name C or name O or name CB )) or resid 387 or (resid 38 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 389 through \ 404 or (resid 405 through 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 440 or (resid 441 through 442 and (name N or name CA \ or name C or name O or name CB )) or resid 443 through 451 or (resid 452 and (n \ ame N or name CA or name C or name O or name CB )) or resid 453 through 458 or ( \ resid 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 477 or (resid 478 and (name N or name CA or name C or name O or name CB \ )) or resid 479 through 483 or (resid 484 and (name N or name CA or name C or na \ me O or name CB )) or resid 485 through 531 or (resid 532 and (name N or name CA \ or name C or name O or name CB )) or resid 533 through 534 or (resid 535 and (n \ ame N or name CA or name C or name O or name CB )) or resid 536 or (resid 537 an \ d (name N or name CA or name C or name O or name CB )) or resid 538 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 or (resid 556 through 558 and (name N or name CA or name C or name O or name \ CB )) or resid 559 through 563 or (resid 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (n \ ame N or name CA or name C or name O or name CB )) or resid 573 through 612 or ( \ resid 613 through 614 and (name N or name CA or name C or name O or name CB )) o \ r resid 615 through 620 or resid 641 through 676 or (resid 690 and (name N or na \ me CA or name C or name O or name CB )) or resid 691 through 736 or (resid 737 a \ nd (name N or name CA or name C or name O or name CB )) or resid 738 through 744 \ or (resid 745 and (name N or name CA or name C or name O or name CB )) or resid \ 746 through 747 or (resid 748 and (name N or name CA or name C or name O or nam \ e CB )) or resid 749 through 754 or (resid 755 and (name N or name CA or name C \ or name O or name CB )) or resid 756 through 775 or (resid 776 and (name N or na \ me CA or name C or name O or name CB )) or resid 777 through 778 or (resid 779 t \ hrough 780 and (name N or name CA or name C or name O or name CB )) or resid 781 \ through 827 or (resid 828 and (name N or name CA or name C or name O or name CB \ )) or (resid 855 and (name N or name CA or name C or name O or name CB )) or re \ sid 856 through 867 or (resid 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 938 or (resid 939 through 944 and (name N or nam \ e CA or name C or name O or name CB )) or resid 945 through 984 or (resid 985 an \ d (name N or name CA or name C or name O or name CB )) or resid 986 through 987 \ or (resid 988 through 989 and (name N or name CA or name C or name O or name CB \ )) or resid 990 through 994 or (resid 995 and (name N or name CA or name C or na \ me O or name CB )) or resid 996 through 1013 or (resid 1014 through 1016 and (na \ me N or name CA or name C or name O or name CB )) or resid 1017 through 1018 or \ (resid 1019 through 1020 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1021 through 1050 or (resid 1051 and (name N or name CA or name C or \ name O or name CB )) or resid 1052 through 1091 or (resid 1092 and (name N or na \ me CA or name C or name O or name CB )) or resid 1093 through 1110 or (resid 111 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1112 through \ 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O or \ name CB )) or resid 1303 through 1319)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 67 or (res \ id 68 through 69 and (name N or name CA or name C or name O or name CB )) or res \ id 70 through 71 or resid 81 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB )) or resid 88 through 107 or (resid 108 through 113 \ and (name N or name CA or name C or name O or name CB )) or resid 114 or (resid \ 115 and (name N or name CA or name C or name O or name CB )) or resid 116 throug \ h 120 or (resid 121 through 124 and (name N or name CA or name C or name O or na \ me CB )) or resid 125 through 142 or (resid 143 through 158 and (name N or name \ CA or name C or name O or name CB )) or resid 159 through 160 or (resid 161 thro \ ugh 164 and (name N or name CA or name C or name O or name CB )) or resid 165 th \ rough 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) \ or resid 189 through 199 or (resid 200 and (name N or name CA or name C or name \ O or name CB )) or resid 201 through 212 or (resid 213 through 214 and (name N \ or name CA or name C or name O or name CB )) or resid 215 through 217 or (resid \ 218 and (name N or name CA or name C or name O or name CB )) or resid 219 throug \ h 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) or \ resid 225 through 248 or (resid 249 through 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 253 or (resid 254 and (name N or n \ ame CA or name C or name O or name CB )) or resid 255 through 320 or (resid 321 \ and (name N or name CA or name C or name O or name CB )) or resid 322 or (resid \ 323 through 324 and (name N or name CA or name C or name O or name CB )) or resi \ d 325 through 331 or (resid 332 and (name N or name CA or name C or name O or na \ me CB )) or resid 333 through 356 or (resid 357 and (name N or name CA or name C \ or name O or name CB )) or resid 358 through 402 or (resid 403 and (name N or n \ ame CA or name C or name O or name CB )) or resid 404 or (resid 405 through 406 \ and (name N or name CA or name C or name O or name CB )) or resid 407 or (resid \ 408 and (name N or name CA or name C or name O or name CB )) or resid 409 throug \ h 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) or \ resid 416 through 423 or (resid 424 and (name N or name CA or name C or name O o \ r name CB )) or resid 425 through 444 or (resid 445 and (name N or name CA or na \ me C or name O or name CB )) or resid 446 through 451 or (resid 452 and (name N \ or name CA or name C or name O or name CB )) or resid 453 through 457 or (resid \ 458 through 459 and (name N or name CA or name C or name O or name CB )) or resi \ d 460 through 464 or (resid 465 and (name N or name CA or name C or name O or na \ me CB )) or resid 466 through 477 or (resid 478 and (name N or name CA or name C \ or name O or name CB )) or resid 479 through 483 or (resid 484 and (name N or n \ ame CA or name C or name O or name CB )) or resid 485 through 486 or (resid 487 \ and (name N or name CA or name C or name O or name CB )) or resid 488 through 49 \ 9 or (resid 500 and (name N or name CA or name C or name O or name CB )) or resi \ d 501 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 534 or (resid 535 and (name N or name CA or name C \ or name O or name CB )) or resid 536 through 563 or (resid 564 and (name N or n \ ame CA or name C or name O or name CB )) or resid 565 through 568 or (resid 569 \ through 572 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 3 through 579 or (resid 580 and (name N or name CA or name C or name O or name C \ B )) or resid 581 through 617 or (resid 618 and (name N or name CA or name C or \ name O or name CB )) or resid 619 through 620 or resid 641 through 747 or (resid \ 748 and (name N or name CA or name C or name O or name CB )) or resid 749 throu \ gh 818 or (resid 819 and (name N or name CA or name C or name O or name CB )) or \ resid 820 through 824 or (resid 825 and (name N or name CA or name C or name O \ or name CB )) or resid 826 through 828 or resid 855 through 917 or (resid 918 an \ d (name N or name CA or name C or name O or name CB )) or resid 919 through 920 \ or (resid 921 and (name N or name CA or name C or name O or name CB )) or resid \ 922 through 932 or (resid 933 and (name N or name CA or name C or name O or name \ CB )) or resid 934 through 935 or (resid 936 and (name N or name CA or name C o \ r name O or name CB )) or resid 937 through 940 or (resid 941 through 944 and (n \ ame N or name CA or name C or name O or name CB )) or resid 945 through 946 or ( \ resid 947 and (name N or name CA or name C or name O or name CB )) or resid 948 \ through 963 or (resid 964 and (name N or name CA or name C or name O or name CB \ )) or resid 965 through 1050 or (resid 1051 and (name N or name CA or name C or \ name O or name CB )) or resid 1052 through 1106 or (resid 1107 and (name N or na \ me CA or name C or name O or name CB )) or resid 1108 through 1110 or (resid 111 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1112 through \ 1137 or (resid 1138 and (name N or name CA or name C or name O or name CB )) or \ resid 1139 through 1143 or (resid 1144 through 1146 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1301 through 1319)) selection = (chain 'C' and (resid 27 through 67 or (resid 68 through 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 or (resid 71 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 94 or (resid 95 throu \ gh 98 and (name N or name CA or name C or name O or name CB )) or resid 99 throu \ gh 107 or (resid 108 through 113 and (name N or name CA or name C or name O or n \ ame CB )) or resid 114 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 135 or (resid 136 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 142 o \ r (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 58 through 175 or (resid 176 through 188 and (name N or name CA or name C or nam \ e O or name CB )) or resid 189 through 199 or (resid 200 and (name N or name CA \ or name C or name O or name CB )) or resid 201 through 205 or (resid 206 and (na \ me N or name CA or name C or name O or name CB )) or resid 207 through 217 or (r \ esid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 t \ hrough 223 or (resid 224 and (name N or name CA or name C or name O or name CB ) \ ) or resid 225 through 244 or (resid 245 through 246 and (name N or name CA or n \ ame C or name O or name CB )) or resid 247 through 248 or (resid 249 through 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 2 \ 80 or (resid 281 and (name N or name CA or name C or name O or name CB )) or res \ id 282 through 286 or (resid 287 through 288 and (name N or name CA or name C or \ name O or name CB )) or resid 289 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 308 or (resid 309 thr \ ough 310 and (name N or name CA or name C or name O or name CB )) or resid 311 t \ hrough 320 or (resid 321 and (name N or name CA or name C or name O or name CB ) \ ) or resid 322 through 323 or (resid 324 and (name N or name CA or name C or nam \ e O or name CB )) or resid 325 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB )) or resid 347 through 368 or (resid 369 and (na \ me N or name CA or name C or name O or name CB )) or resid 370 through 385 or (r \ esid 386 and (name N or name CA or name C or name O or name CB )) or resid 387 t \ hrough 402 or (resid 403 and (name N or name CA or name C or name O or name CB ) \ ) or resid 404 through 407 or (resid 408 and (name N or name CA or name C or nam \ e O or name CB )) or resid 409 through 416 or (resid 417 and (name N or name CA \ or name C or name O or name CB )) or resid 418 through 423 or (resid 424 and (na \ me N or name CA or name C or name O or name CB )) or resid 425 through 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB )) or resid 429 t \ hrough 438 or (resid 439 through 442 and (name N or name CA or name C or name O \ or name CB )) or resid 443 through 444 or (resid 445 and (name N or name CA or n \ ame C or name O or name CB )) or resid 446 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 508 or (resid \ 509 and (name N or name CA or name C or name O or name CB )) or resid 510 throu \ gh 531 or (resid 532 and (name N or name CA or name C or name O or name CB )) or \ resid 533 through 536 or (resid 537 and (name N or name CA or name C or name O \ or name CB )) or resid 538 through 556 or (resid 557 through 558 and (name N or \ name CA or name C or name O or name CB )) or resid 559 through 568 or (resid 569 \ through 572 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 73 through 612 or (resid 613 through 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 662 or (resid 663 and (name N or name CA \ or name C or name O or name CB )) or resid 664 through 701 or (resid 702 and (na \ me N or name CA or name C or name O or name CB )) or resid 703 through 736 or (r \ esid 737 and (name N or name CA or name C or name O or name CB )) or resid 738 t \ hrough 739 or (resid 740 and (name N or name CA or name C or name O or name CB ) \ ) or resid 741 through 744 or (resid 745 and (name N or name CA or name C or nam \ e O or name CB )) or resid 746 through 754 or (resid 755 and (name N or name CA \ or name C or name O or name CB )) or resid 756 through 775 or (resid 776 and (na \ me N or name CA or name C or name O or name CB )) or resid 777 through 778 or (r \ esid 779 through 780 and (name N or name CA or name C or name O or name CB )) or \ resid 781 through 794 or (resid 795 and (name N or name CA or name C or name O \ or name CB )) or resid 796 through 807 or (resid 808 and (name N or name CA or n \ ame C or name O or name CB )) or resid 809 through 818 or (resid 819 and (name N \ or name CA or name C or name O or name CB )) or resid 820 through 824 or (resid \ 825 and (name N or name CA or name C or name O or name CB )) or resid 826 throu \ gh 828 or (resid 855 and (name N or name CA or name C or name O or name CB )) or \ resid 856 through 867 or (resid 868 and (name N or name CA or name C or name O \ or name CB )) or resid 869 through 917 or (resid 918 and (name N or name CA or n \ ame C or name O or name CB )) or resid 919 through 938 or (resid 939 through 944 \ and (name N or name CA or name C or name O or name CB )) or resid 945 through 9 \ 46 or (resid 947 and (name N or name CA or name C or name O or name CB )) or res \ id 948 through 963 or (resid 964 and (name N or name CA or name C or name O or n \ ame CB )) or resid 965 through 994 or (resid 995 and (name N or name CA or name \ C or name O or name CB )) or resid 996 through 1013 or (resid 1014 through 1016 \ and (name N or name CA or name C or name O or name CB )) or resid 1017 through 1 \ 018 or (resid 1019 through 1020 and (name N or name CA or name C or name O or na \ me CB )) or resid 1021 through 1072 or (resid 1073 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1074 through 1091 or (resid 1092 and (name \ N or name CA or name C or name O or name CB )) or resid 1093 through 1137 or (re \ sid 1138 and (name N or name CA or name C or name O or name CB )) or resid 1139 \ through 1140 or (resid 1141 through 1142 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1143 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1301 through 1319)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'O' selection = chain 'P' } ncs_group { reference = (chain 'F' and ((resid 1 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 17 or (resid 18 through 2 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 22 through 4 \ 2 or (resid 43 and (name N or name CA or name C or name O or name CB )) or resid \ 44 through 82 or (resid 82A through 82C and (name N or name CA or name C or nam \ e O or name CB )) or resid 83 or (resid 84 through 85 and (name N or name CA or \ name C or name O or name CB )) or resid 86 or (resid 87 through 89 and (name N o \ r name CA or name C or name O or name CB )) or resid 90 through 96 or (resid 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 through 100 \ or (resid 100A and (name N or name CA or name C or name O or name CB )) or resi \ d 100B through 113)) selection = (chain 'H' and ((resid 1 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 50 or (resid \ 51 and (name N or name CA or name C or name O or name CB )) or resid 52 through \ 52A or (resid 53 and (name N or name CA or name C or name O or name CB )) or re \ sid 54 through 67 or (resid 68 and (name N or name CA or name C or name O or nam \ e CB )) or resid 69 through 86 or (resid 87 through 89 and (name N or name CA or \ name C or name O or name CB )) or resid 90 through 95 or (resid 96 through 97 a \ nd (name N or name CA or name C or name O or name CB )) or resid 98 through 112 \ or (resid 113 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 1 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB )) or resid 22 through 29 or (resid 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 through 42 or (resid 43 and (n \ ame N or name CA or name C or name O or name CB )) or resid 44 through 50 or (re \ sid 51 and (name N or name CA or name C or name O or name CB )) or resid 52 thro \ ugh 52A or (resid 53 and (name N or name CA or name C or name O or name CB )) or \ resid 54 through 65 or (resid 66 through 68 and (name N or name CA or name C or \ name O or name CB )) or resid 69 through 94 or (resid 95 through 97 and (name N \ or name CA or name C or name O or name CB )) or resid 98 through 113)) } ncs_group { reference = (chain 'G' and (resid 3 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 23 or (resid 24 and (name \ N or name CA or name C or name O or name CB )) or (resid 25 through 27A and (nam \ e N or name CA or name C or name O or name CB )) or resid 27B through 47 or (res \ id 48 and (name N or name CA or name C or name O or name CB )) or resid 49 throu \ gh 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or r \ esid 68 through 73 or (resid 74 through 76 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 77 through 84 and (name N or name CA or name C or \ name O or name CB )) or resid 85 through 107)) selection = (chain 'K' and (resid 3 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 25 or (resid 26 through 27 \ A and (name N or name CA or name C or name O or name CB )) or resid 27B through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or resi \ d 77 through 95 or (resid 95A and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 101 or (resid 102 through 107 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'L' and (resid 3 through 25 or (resid 26 through 27A and (name N or name \ CA or name C or name O or name CB )) or resid 27B through 47 or (resid 48 and (n \ ame N or name CA or name C or name O or name CB )) or resid 49 through 101 or (r \ esid 102 through 107 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.900 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29252 Z= 0.258 Angle : 0.874 12.156 40177 Z= 0.489 Chirality : 0.056 0.578 4783 Planarity : 0.006 0.073 5118 Dihedral : 14.056 111.706 10661 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 0.26 % Allowed : 0.44 % Favored : 99.30 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.13), residues: 3734 helix: -0.57 (0.18), residues: 691 sheet: -0.93 (0.16), residues: 905 loop : -1.62 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 765 TYR 0.029 0.002 TYR J 32 PHE 0.037 0.002 PHE A 238 TRP 0.023 0.002 TRP L 35 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00534 (29144) covalent geometry : angle 0.84649 (39898) SS BOND : bond 0.00509 ( 45) SS BOND : angle 2.04408 ( 90) hydrogen bonds : bond 0.20552 ( 1061) hydrogen bonds : angle 9.19303 ( 2928) link_BETA1-4 : bond 0.00944 ( 15) link_BETA1-4 : angle 3.13687 ( 45) link_NAG-ASN : bond 0.00484 ( 48) link_NAG-ASN : angle 2.97926 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 690 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7513 (tp40) REVERT: B 900 MET cc_start: 0.7958 (mtp) cc_final: 0.7626 (mtp) REVERT: F 43 GLN cc_start: 0.7744 (pp30) cc_final: 0.7453 (pp30) REVERT: F 45 LEU cc_start: 0.8533 (tp) cc_final: 0.8228 (tp) REVERT: F 48 MET cc_start: 0.7320 (mpp) cc_final: 0.6881 (mpp) REVERT: G 24 THR cc_start: 0.8802 (t) cc_final: 0.8520 (p) REVERT: G 49 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7390 (p90) REVERT: H 51 ILE cc_start: 0.8167 (tp) cc_final: 0.7786 (mm) REVERT: H 61 GLN cc_start: 0.8188 (tp40) cc_final: 0.7864 (tp40) REVERT: H 69 MET cc_start: 0.7927 (mtm) cc_final: 0.7708 (mtm) REVERT: H 100 MET cc_start: 0.7846 (mtp) cc_final: 0.7632 (mtp) REVERT: J 48 MET cc_start: 0.6797 (mpp) cc_final: 0.6371 (mpp) REVERT: K 47 MET cc_start: 0.7389 (mmm) cc_final: 0.7179 (mmm) REVERT: L 37 GLN cc_start: 0.8675 (tt0) cc_final: 0.8221 (tt0) REVERT: L 85 ASP cc_start: 0.7701 (p0) cc_final: 0.7356 (p0) outliers start: 7 outliers final: 2 residues processed: 153 average time/residue: 0.1701 time to fit residues: 44.2842 Evaluate side-chains 131 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain G residue 49 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS C 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.048283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.039543 restraints weight = 148119.560| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.50 r_work: 0.2974 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29252 Z= 0.173 Angle : 0.619 9.926 40177 Z= 0.319 Chirality : 0.046 0.293 4783 Planarity : 0.004 0.063 5118 Dihedral : 8.869 69.723 5349 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer: Outliers : 0.37 % Allowed : 4.69 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 3734 helix: 0.50 (0.20), residues: 669 sheet: -0.63 (0.16), residues: 923 loop : -1.40 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.025 0.001 TYR F 27 PHE 0.015 0.001 PHE B 86 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00372 (29144) covalent geometry : angle 0.59434 (39898) SS BOND : bond 0.00275 ( 45) SS BOND : angle 1.26783 ( 90) hydrogen bonds : bond 0.04232 ( 1061) hydrogen bonds : angle 6.45622 ( 2928) link_BETA1-4 : bond 0.00506 ( 15) link_BETA1-4 : angle 2.45955 ( 45) link_NAG-ASN : bond 0.00360 ( 48) link_NAG-ASN : angle 2.49088 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.061 Fit side-chains REVERT: A 690 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: A 1040 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7801 (p) REVERT: B 258 TRP cc_start: 0.2946 (t60) cc_final: 0.2670 (t60) REVERT: F 43 GLN cc_start: 0.7950 (pp30) cc_final: 0.7589 (pp30) REVERT: H 61 GLN cc_start: 0.8368 (tp40) cc_final: 0.8047 (tp40) REVERT: H 69 MET cc_start: 0.8177 (mtm) cc_final: 0.7919 (mtm) REVERT: H 103 TRP cc_start: 0.8886 (m-10) cc_final: 0.8584 (m100) REVERT: J 27 TYR cc_start: 0.8554 (p90) cc_final: 0.8281 (p90) REVERT: J 48 MET cc_start: 0.6873 (mpp) cc_final: 0.6506 (mpp) REVERT: K 37 GLN cc_start: 0.8706 (tt0) cc_final: 0.8422 (tt0) REVERT: K 47 MET cc_start: 0.7652 (mmm) cc_final: 0.7452 (mmm) REVERT: K 54 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.8269 (mtt90) REVERT: L 35 TRP cc_start: 0.7606 (m-10) cc_final: 0.7313 (m-10) REVERT: L 37 GLN cc_start: 0.8772 (tt0) cc_final: 0.8481 (tt0) outliers start: 10 outliers final: 5 residues processed: 139 average time/residue: 0.1790 time to fit residues: 41.5328 Evaluate side-chains 127 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 341 optimal weight: 7.9990 chunk 6 optimal weight: 0.0980 chunk 323 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 368 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 371 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN ** G 39 HIS ** 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 = 0.3396 r_free = 0.3396 target = 0.048207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.039351 restraints weight = 148018.282| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.59 r_work: 0.2968 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29252 Z= 0.212 Angle : 0.610 10.301 40177 Z= 0.311 Chirality : 0.046 0.283 4783 Planarity : 0.004 0.060 5118 Dihedral : 7.570 59.832 5346 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.03 % Favored : 94.91 % Rotamer: Outliers : 0.77 % Allowed : 6.33 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3734 helix: 0.77 (0.21), residues: 665 sheet: -0.56 (0.16), residues: 925 loop : -1.27 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.025 0.002 TYR A1067 PHE 0.025 0.002 PHE A1052 TRP 0.011 0.002 TRP F 36 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00469 (29144) covalent geometry : angle 0.58718 (39898) SS BOND : bond 0.00287 ( 45) SS BOND : angle 1.06203 ( 90) hydrogen bonds : bond 0.03990 ( 1061) hydrogen bonds : angle 5.95964 ( 2928) link_BETA1-4 : bond 0.00513 ( 15) link_BETA1-4 : angle 2.34807 ( 45) link_NAG-ASN : bond 0.00365 ( 48) link_NAG-ASN : angle 2.42084 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.105 Fit side-chains REVERT: A 1040 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7881 (p) REVERT: F 43 GLN cc_start: 0.8022 (pp30) cc_final: 0.7660 (pp30) REVERT: H 61 GLN cc_start: 0.8428 (tp40) cc_final: 0.8119 (tp40) REVERT: H 69 MET cc_start: 0.8258 (mtm) cc_final: 0.8007 (mtm) REVERT: H 87 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8053 (p) REVERT: H 103 TRP cc_start: 0.8894 (m-10) cc_final: 0.8547 (m100) REVERT: J 48 MET cc_start: 0.6918 (mpp) cc_final: 0.6523 (mpp) REVERT: K 37 GLN cc_start: 0.8688 (tt0) cc_final: 0.8303 (tt0) REVERT: K 54 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8295 (mtt90) REVERT: L 35 TRP cc_start: 0.7646 (m-10) cc_final: 0.7311 (m-10) REVERT: L 37 GLN cc_start: 0.8750 (tt0) cc_final: 0.8365 (tt0) REVERT: L 54 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7455 (mtt-85) REVERT: L 91 TYR cc_start: 0.5935 (t80) cc_final: 0.5519 (t80) outliers start: 21 outliers final: 12 residues processed: 139 average time/residue: 0.1730 time to fit residues: 40.9779 Evaluate side-chains 134 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 216 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 360 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 364 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 658 ASN C1088 HIS ** G 39 HIS ** 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 = 0.3365 r_free = 0.3365 target = 0.047203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.038388 restraints weight = 147280.495| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.53 r_work: 0.2934 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 29252 Z= 0.330 Angle : 0.682 10.696 40177 Z= 0.347 Chirality : 0.048 0.294 4783 Planarity : 0.004 0.058 5118 Dihedral : 7.121 59.454 5343 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 1.43 % Allowed : 8.68 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3734 helix: 0.86 (0.21), residues: 645 sheet: -0.65 (0.16), residues: 942 loop : -1.29 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.029 0.002 TYR A 170 PHE 0.026 0.002 PHE B 168 TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00731 (29144) covalent geometry : angle 0.65919 (39898) SS BOND : bond 0.00395 ( 45) SS BOND : angle 1.11778 ( 90) hydrogen bonds : bond 0.04100 ( 1061) hydrogen bonds : angle 5.88467 ( 2928) link_BETA1-4 : bond 0.00568 ( 15) link_BETA1-4 : angle 2.31599 ( 45) link_NAG-ASN : bond 0.00542 ( 48) link_NAG-ASN : angle 2.59847 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.260 Fit side-chains REVERT: F 43 GLN cc_start: 0.7873 (pp30) cc_final: 0.7565 (pp30) REVERT: H 61 GLN cc_start: 0.8498 (tp40) cc_final: 0.8216 (tp40) REVERT: H 69 MET cc_start: 0.8169 (mtm) cc_final: 0.7932 (mtm) REVERT: J 48 MET cc_start: 0.6889 (mpp) cc_final: 0.6524 (mpp) REVERT: J 80 MET cc_start: 0.8476 (tmm) cc_final: 0.7959 (tmm) REVERT: J 100 VAL cc_start: 0.8920 (m) cc_final: 0.8608 (t) REVERT: K 37 GLN cc_start: 0.8716 (tt0) cc_final: 0.8133 (tt0) REVERT: K 54 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8284 (mtt90) REVERT: L 35 TRP cc_start: 0.7735 (m-10) cc_final: 0.7386 (m-10) REVERT: L 37 GLN cc_start: 0.8740 (tt0) cc_final: 0.8350 (tt0) REVERT: L 54 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7542 (mtt-85) outliers start: 39 outliers final: 26 residues processed: 148 average time/residue: 0.1695 time to fit residues: 42.9039 Evaluate side-chains 143 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 39 HIS Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 109 optimal weight: 10.0000 chunk 326 optimal weight: 0.0370 chunk 320 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 352 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 315 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.047529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.038722 restraints weight = 146752.579| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.54 r_work: 0.2947 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29252 Z= 0.258 Angle : 0.625 10.631 40177 Z= 0.318 Chirality : 0.047 0.286 4783 Planarity : 0.004 0.055 5118 Dihedral : 6.656 57.873 5343 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.46 % Rotamer: Outliers : 1.61 % Allowed : 9.41 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3734 helix: 0.99 (0.21), residues: 646 sheet: -0.63 (0.17), residues: 927 loop : -1.24 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 94 TYR 0.023 0.002 TYR A1067 PHE 0.018 0.002 PHE B 86 TRP 0.014 0.001 TRP A 104 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00571 (29144) covalent geometry : angle 0.60264 (39898) SS BOND : bond 0.00339 ( 45) SS BOND : angle 1.05454 ( 90) hydrogen bonds : bond 0.03831 ( 1061) hydrogen bonds : angle 5.71479 ( 2928) link_BETA1-4 : bond 0.00514 ( 15) link_BETA1-4 : angle 2.21195 ( 45) link_NAG-ASN : bond 0.00415 ( 48) link_NAG-ASN : angle 2.46536 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 1.104 Fit side-chains REVERT: F 43 GLN cc_start: 0.7943 (pp30) cc_final: 0.7630 (pp30) REVERT: H 61 GLN cc_start: 0.8516 (tp40) cc_final: 0.8220 (tp40) REVERT: H 69 MET cc_start: 0.8127 (mtm) cc_final: 0.7916 (mtm) REVERT: J 48 MET cc_start: 0.6860 (mpp) cc_final: 0.6511 (mpp) REVERT: J 69 MET cc_start: 0.8162 (mtm) cc_final: 0.7897 (mtm) REVERT: J 80 MET cc_start: 0.8509 (tmm) cc_final: 0.7928 (tmm) REVERT: J 100 VAL cc_start: 0.8902 (m) cc_final: 0.8458 (t) REVERT: J 100 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6457 (mmm) REVERT: K 37 GLN cc_start: 0.8677 (tt0) cc_final: 0.8084 (tt0) REVERT: K 54 ARG cc_start: 0.8640 (mtm-85) cc_final: 0.8380 (mtt90) REVERT: L 35 TRP cc_start: 0.7733 (m-10) cc_final: 0.7352 (m-10) REVERT: L 37 GLN cc_start: 0.8743 (tt0) cc_final: 0.8335 (tt0) REVERT: L 54 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7582 (mtt-85) outliers start: 44 outliers final: 27 residues processed: 154 average time/residue: 0.1666 time to fit residues: 43.8133 Evaluate side-chains 144 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 109 optimal weight: 6.9990 chunk 287 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 326 optimal weight: 0.0770 chunk 219 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.048481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.039856 restraints weight = 146018.581| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.42 r_work: 0.2992 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29252 Z= 0.134 Angle : 0.557 11.173 40177 Z= 0.284 Chirality : 0.045 0.276 4783 Planarity : 0.004 0.053 5118 Dihedral : 6.041 59.948 5343 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.29 % Rotamer: Outliers : 1.28 % Allowed : 10.58 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3734 helix: 1.24 (0.21), residues: 647 sheet: -0.49 (0.17), residues: 908 loop : -1.16 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.021 0.001 TYR A1067 PHE 0.017 0.001 PHE A 238 TRP 0.014 0.001 TRP A 104 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00293 (29144) covalent geometry : angle 0.53753 (39898) SS BOND : bond 0.00426 ( 45) SS BOND : angle 0.93834 ( 90) hydrogen bonds : bond 0.03433 ( 1061) hydrogen bonds : angle 5.47458 ( 2928) link_BETA1-4 : bond 0.00469 ( 15) link_BETA1-4 : angle 2.00760 ( 45) link_NAG-ASN : bond 0.00243 ( 48) link_NAG-ASN : angle 2.19939 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.048 Fit side-chains REVERT: B 869 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8683 (mtp) REVERT: B 900 MET cc_start: 0.8413 (mtp) cc_final: 0.8143 (mtp) REVERT: H 61 GLN cc_start: 0.8460 (tp40) cc_final: 0.8141 (tp40) REVERT: H 87 THR cc_start: 0.8564 (m) cc_final: 0.8233 (p) REVERT: J 47 TRP cc_start: 0.7429 (t60) cc_final: 0.7041 (t60) REVERT: J 48 MET cc_start: 0.6814 (mpp) cc_final: 0.6296 (mpp) REVERT: J 69 MET cc_start: 0.8047 (mtm) cc_final: 0.7822 (mtm) REVERT: J 80 MET cc_start: 0.8486 (tmm) cc_final: 0.7952 (tmm) REVERT: K 37 GLN cc_start: 0.8639 (tt0) cc_final: 0.8133 (tt0) REVERT: K 54 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8354 (mtt90) REVERT: L 35 TRP cc_start: 0.7717 (m-10) cc_final: 0.7345 (m-10) REVERT: L 37 GLN cc_start: 0.8716 (tt0) cc_final: 0.8342 (tt0) REVERT: L 54 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7457 (mtt-85) outliers start: 35 outliers final: 21 residues processed: 147 average time/residue: 0.1629 time to fit residues: 41.0891 Evaluate side-chains 138 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 111 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 chunk 266 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN ** G 39 HIS ** 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 = 0.3401 r_free = 0.3401 target = 0.048335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.039703 restraints weight = 146037.127| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.41 r_work: 0.2987 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29252 Z= 0.161 Angle : 0.566 11.486 40177 Z= 0.287 Chirality : 0.045 0.260 4783 Planarity : 0.004 0.051 5118 Dihedral : 5.850 57.285 5343 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 1.65 % Allowed : 10.77 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3734 helix: 1.27 (0.21), residues: 647 sheet: -0.46 (0.17), residues: 908 loop : -1.14 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 83 TYR 0.028 0.001 TYR K 91 PHE 0.017 0.001 PHE C 486 TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00357 (29144) covalent geometry : angle 0.54685 (39898) SS BOND : bond 0.00227 ( 45) SS BOND : angle 0.90312 ( 90) hydrogen bonds : bond 0.03441 ( 1061) hydrogen bonds : angle 5.40157 ( 2928) link_BETA1-4 : bond 0.00495 ( 15) link_BETA1-4 : angle 1.97551 ( 45) link_NAG-ASN : bond 0.00278 ( 48) link_NAG-ASN : angle 2.19934 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 1.025 Fit side-chains REVERT: B 869 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8700 (mtp) REVERT: B 900 MET cc_start: 0.8429 (mtp) cc_final: 0.8209 (mtp) REVERT: H 61 GLN cc_start: 0.8474 (tp40) cc_final: 0.8158 (tp40) REVERT: H 87 THR cc_start: 0.8575 (m) cc_final: 0.8265 (p) REVERT: J 37 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8162 (m) REVERT: J 47 TRP cc_start: 0.7448 (t60) cc_final: 0.6996 (t60) REVERT: J 48 MET cc_start: 0.6830 (mpp) cc_final: 0.6319 (mpp) REVERT: J 69 MET cc_start: 0.8087 (mtm) cc_final: 0.7833 (mtm) REVERT: J 80 MET cc_start: 0.8505 (tmm) cc_final: 0.7934 (tmm) REVERT: J 100 VAL cc_start: 0.8879 (m) cc_final: 0.8585 (t) REVERT: J 100 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6508 (mmm) REVERT: K 37 GLN cc_start: 0.8626 (tt0) cc_final: 0.8076 (tt0) REVERT: K 54 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8336 (mtt90) REVERT: L 35 TRP cc_start: 0.7692 (m-10) cc_final: 0.7217 (m-10) REVERT: L 37 GLN cc_start: 0.8695 (tt0) cc_final: 0.8261 (tt0) REVERT: L 47 MET cc_start: 0.7880 (mmm) cc_final: 0.7636 (mmm) REVERT: L 54 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7471 (mtt-85) outliers start: 45 outliers final: 30 residues processed: 153 average time/residue: 0.1674 time to fit residues: 43.3047 Evaluate side-chains 151 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 39 HIS Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 356 optimal weight: 0.4980 chunk 369 optimal weight: 0.0030 chunk 0 optimal weight: 7.9990 chunk 329 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 306 optimal weight: 0.9980 chunk 187 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 175 optimal weight: 0.0980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.049218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.040457 restraints weight = 146163.370| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.56 r_work: 0.3015 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29252 Z= 0.096 Angle : 0.543 12.250 40177 Z= 0.274 Chirality : 0.044 0.274 4783 Planarity : 0.004 0.051 5118 Dihedral : 5.436 56.703 5343 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 1.43 % Allowed : 11.35 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3734 helix: 1.56 (0.22), residues: 633 sheet: -0.32 (0.17), residues: 888 loop : -1.08 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.023 0.001 TYR K 91 PHE 0.015 0.001 PHE A 238 TRP 0.019 0.001 TRP J 103 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00203 (29144) covalent geometry : angle 0.52590 (39898) SS BOND : bond 0.00203 ( 45) SS BOND : angle 0.95541 ( 90) hydrogen bonds : bond 0.03196 ( 1061) hydrogen bonds : angle 5.23468 ( 2928) link_BETA1-4 : bond 0.00518 ( 15) link_BETA1-4 : angle 1.81834 ( 45) link_NAG-ASN : bond 0.00193 ( 48) link_NAG-ASN : angle 2.00801 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.944 Fit side-chains REVERT: A 697 MET cc_start: 0.8846 (ptm) cc_final: 0.8557 (ptm) REVERT: B 468 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8921 (tp) REVERT: B 869 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8677 (mtp) REVERT: B 900 MET cc_start: 0.8456 (mtp) cc_final: 0.8203 (mtp) REVERT: H 32 TYR cc_start: 0.8188 (m-10) cc_final: 0.7909 (m-10) REVERT: H 61 GLN cc_start: 0.8467 (tp40) cc_final: 0.8146 (tp40) REVERT: H 69 MET cc_start: 0.8112 (mtm) cc_final: 0.7813 (mtm) REVERT: H 87 THR cc_start: 0.8611 (m) cc_final: 0.8327 (p) REVERT: H 98 TRP cc_start: 0.8676 (t-100) cc_final: 0.8146 (t-100) REVERT: H 103 TRP cc_start: 0.8773 (m-10) cc_final: 0.8411 (m100) REVERT: J 47 TRP cc_start: 0.7400 (t60) cc_final: 0.6766 (t60) REVERT: J 48 MET cc_start: 0.6864 (mpp) cc_final: 0.6394 (mpp) REVERT: J 80 MET cc_start: 0.8519 (tmm) cc_final: 0.7970 (tmm) REVERT: J 100 VAL cc_start: 0.8770 (m) cc_final: 0.8474 (t) REVERT: J 100 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6478 (mmm) REVERT: K 37 GLN cc_start: 0.8617 (tt0) cc_final: 0.8112 (tt0) REVERT: K 98 PHE cc_start: 0.8456 (m-10) cc_final: 0.8214 (m-10) REVERT: L 35 TRP cc_start: 0.7702 (m-10) cc_final: 0.7234 (m-10) REVERT: L 37 GLN cc_start: 0.8722 (tt0) cc_final: 0.8240 (tt0) REVERT: L 54 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7375 (mtt-85) outliers start: 39 outliers final: 26 residues processed: 156 average time/residue: 0.1709 time to fit residues: 44.5290 Evaluate side-chains 157 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 285 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS C 658 ASN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.048050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039252 restraints weight = 146509.968| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.52 r_work: 0.2969 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29252 Z= 0.223 Angle : 0.599 11.810 40177 Z= 0.301 Chirality : 0.045 0.244 4783 Planarity : 0.004 0.051 5118 Dihedral : 5.618 55.509 5343 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.54 % Rotamer: Outliers : 1.43 % Allowed : 11.50 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3734 helix: 1.31 (0.21), residues: 647 sheet: -0.40 (0.17), residues: 928 loop : -1.10 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 71 TYR 0.021 0.002 TYR F 27 PHE 0.018 0.002 PHE C 86 TRP 0.016 0.001 TRP B 258 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00497 (29144) covalent geometry : angle 0.58051 (39898) SS BOND : bond 0.00274 ( 45) SS BOND : angle 1.00988 ( 90) hydrogen bonds : bond 0.03516 ( 1061) hydrogen bonds : angle 5.31805 ( 2928) link_BETA1-4 : bond 0.00529 ( 15) link_BETA1-4 : angle 1.96664 ( 45) link_NAG-ASN : bond 0.00374 ( 48) link_NAG-ASN : angle 2.19285 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 973 ILE cc_start: 0.8953 (pt) cc_final: 0.8723 (tt) REVERT: B 869 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8615 (mtp) REVERT: C 902 MET cc_start: 0.8627 (mmm) cc_final: 0.8319 (mmm) REVERT: H 61 GLN cc_start: 0.8518 (tp40) cc_final: 0.8236 (tp40) REVERT: H 69 MET cc_start: 0.8247 (mtm) cc_final: 0.8006 (ptm) REVERT: H 103 TRP cc_start: 0.8828 (m-10) cc_final: 0.8463 (m100) REVERT: J 47 TRP cc_start: 0.7531 (t60) cc_final: 0.6920 (t60) REVERT: J 48 MET cc_start: 0.6930 (mpp) cc_final: 0.6333 (mpp) REVERT: J 80 MET cc_start: 0.8504 (tmm) cc_final: 0.7923 (tmm) REVERT: J 100 VAL cc_start: 0.8889 (m) cc_final: 0.8590 (t) REVERT: J 100 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6462 (mmm) REVERT: K 37 GLN cc_start: 0.8608 (tt0) cc_final: 0.8095 (tt0) REVERT: K 98 PHE cc_start: 0.8473 (m-10) cc_final: 0.8233 (m-10) REVERT: L 35 TRP cc_start: 0.7744 (m100) cc_final: 0.7276 (m-10) REVERT: L 37 GLN cc_start: 0.8787 (tt0) cc_final: 0.8265 (tt0) REVERT: L 54 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7551 (mtt-85) outliers start: 39 outliers final: 33 residues processed: 151 average time/residue: 0.1638 time to fit residues: 42.2325 Evaluate side-chains 158 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 253 optimal weight: 6.9990 chunk 296 optimal weight: 1.9990 chunk 338 optimal weight: 0.0980 chunk 281 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 362 optimal weight: 20.0000 chunk 232 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.048712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.040082 restraints weight = 145349.938| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.41 r_work: 0.3002 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29252 Z= 0.134 Angle : 0.560 12.093 40177 Z= 0.281 Chirality : 0.044 0.263 4783 Planarity : 0.004 0.057 5118 Dihedral : 5.410 55.891 5343 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 1.35 % Allowed : 11.83 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3734 helix: 1.54 (0.21), residues: 633 sheet: -0.39 (0.17), residues: 910 loop : -1.07 (0.14), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 83 TYR 0.020 0.001 TYR A1067 PHE 0.014 0.001 PHE A 238 TRP 0.015 0.001 TRP A 104 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00297 (29144) covalent geometry : angle 0.54284 (39898) SS BOND : bond 0.00187 ( 45) SS BOND : angle 0.91350 ( 90) hydrogen bonds : bond 0.03306 ( 1061) hydrogen bonds : angle 5.22790 ( 2928) link_BETA1-4 : bond 0.00513 ( 15) link_BETA1-4 : angle 1.85255 ( 45) link_NAG-ASN : bond 0.00239 ( 48) link_NAG-ASN : angle 2.05970 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: B 468 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8851 (tp) REVERT: B 900 MET cc_start: 0.8403 (mtp) cc_final: 0.8178 (mtp) REVERT: H 32 TYR cc_start: 0.8195 (m-10) cc_final: 0.7909 (m-10) REVERT: H 61 GLN cc_start: 0.8509 (tp40) cc_final: 0.8215 (tp40) REVERT: H 87 THR cc_start: 0.8610 (m) cc_final: 0.8330 (p) REVERT: H 98 TRP cc_start: 0.8705 (t-100) cc_final: 0.8215 (t-100) REVERT: H 103 TRP cc_start: 0.8796 (m-10) cc_final: 0.8426 (m100) REVERT: J 37 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8115 (m) REVERT: J 47 TRP cc_start: 0.7488 (t60) cc_final: 0.6818 (t60) REVERT: J 48 MET cc_start: 0.6865 (mpp) cc_final: 0.6404 (mpp) REVERT: J 80 MET cc_start: 0.8494 (tmm) cc_final: 0.7790 (tmm) REVERT: J 100 VAL cc_start: 0.8843 (m) cc_final: 0.8603 (t) REVERT: J 100 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6468 (mmm) REVERT: K 37 GLN cc_start: 0.8590 (tt0) cc_final: 0.8085 (tt0) REVERT: K 98 PHE cc_start: 0.8397 (m-10) cc_final: 0.8185 (m-10) REVERT: L 35 TRP cc_start: 0.7763 (m100) cc_final: 0.7298 (m-10) REVERT: L 37 GLN cc_start: 0.8692 (tt0) cc_final: 0.8053 (tt0) REVERT: L 47 MET cc_start: 0.7891 (mmm) cc_final: 0.7547 (mmm) REVERT: L 54 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7460 (mtt-85) outliers start: 37 outliers final: 31 residues processed: 149 average time/residue: 0.1685 time to fit residues: 42.6906 Evaluate side-chains 156 residues out of total 3266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 351 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 268 optimal weight: 0.0270 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN ** G 39 HIS ** 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 = 0.3402 r_free = 0.3402 target = 0.048357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.039704 restraints weight = 146466.976| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.41 r_work: 0.2988 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29252 Z= 0.177 Angle : 0.573 12.094 40177 Z= 0.288 Chirality : 0.045 0.248 4783 Planarity : 0.004 0.050 5118 Dihedral : 5.422 55.620 5343 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 1.50 % Allowed : 11.75 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3734 helix: 1.36 (0.21), residues: 647 sheet: -0.39 (0.17), residues: 909 loop : -1.07 (0.14), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.020 0.001 TYR F 27 PHE 0.014 0.001 PHE C 86 TRP 0.014 0.001 TRP J 103 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00393 (29144) covalent geometry : angle 0.55566 (39898) SS BOND : bond 0.00226 ( 45) SS BOND : angle 0.93957 ( 90) hydrogen bonds : bond 0.03395 ( 1061) hydrogen bonds : angle 5.24143 ( 2928) link_BETA1-4 : bond 0.00518 ( 15) link_BETA1-4 : angle 1.90260 ( 45) link_NAG-ASN : bond 0.00294 ( 48) link_NAG-ASN : angle 2.10892 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5264.56 seconds wall clock time: 91 minutes 28.70 seconds (5488.70 seconds total)