Starting phenix.real_space_refine on Tue May 27 20:00:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xic_33202/05_2025/7xic_33202.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xic_33202/05_2025/7xic_33202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xic_33202/05_2025/7xic_33202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xic_33202/05_2025/7xic_33202.map" model { file = "/net/cci-nas-00/data/ceres_data/7xic_33202/05_2025/7xic_33202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xic_33202/05_2025/7xic_33202.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.085 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 19039 2.51 5 N 4908 2.21 5 O 5859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.52s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29941 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7848 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.27, per 1000 atoms: 0.58 Number of scatterers: 29941 At special positions: 0 Unit cell: (168.485, 160.876, 194.573, 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 5859 8.00 N 4908 7.00 C 19039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.19 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.97 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.12 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.00 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.15 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.07 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.15 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.15 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.10 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.12 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.00 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.14 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.07 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.20 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.17 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.18 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.12 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.00 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.07 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 102 " - pdb=" SG CYS E 106 " distance=2.09 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 106 " distance=2.09 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 102 " - pdb=" SG CYS K 106 " distance=2.09 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 A1406 " - " NAG A1407 " " NAG B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " NAG C1406 " - " NAG C1407 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Time building additional restraints: 8.28 Conformation dependent library (CDL) restraints added in 3.4 seconds 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 60 sheets defined 22.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.689A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.479A 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 438 through 443 removed outlier: 3.542A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.530A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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: 3.790A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.702A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (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 349 through 353 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.686A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.589A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.688A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.478A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A 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 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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: 3.810A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.514A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.395A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.326A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.469A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 5.676A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.292A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A 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: 3.543A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A 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: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.768A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.851A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.589A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.471A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.512A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.696A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.857A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.239A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.577A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.546A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.943A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.685A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.738A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.478A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 328 removed outlier: 5.456A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.307A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.286A pdb=" N GLY E 33 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.629A pdb=" N TYR E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.551A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.287A pdb=" N GLY H 33 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.630A pdb=" N TYR H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.550A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.286A pdb=" N GLY K 33 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.630A pdb=" N TYR K 117 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.550A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 1181 hydrogen bonds defined for protein. 3117 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: 13.82 Time building geometry restraints manager: 9.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6644 1.33 - 1.45: 8265 1.45 - 1.58: 15539 1.58 - 1.71: 0 1.71 - 1.84: 171 Bond restraints: 30619 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.20e-02 6.94e+03 4.40e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.36e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.07e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" N PRO B 521 " pdb=" CD PRO B 521 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.87e+01 ... (remaining 30614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 39963 2.63 - 5.26: 1533 5.26 - 7.89: 94 7.89 - 10.53: 18 10.53 - 13.16: 12 Bond angle restraints: 41620 Sorted by residual: angle pdb=" N PHE A 375 " pdb=" CA PHE A 375 " pdb=" C PHE A 375 " ideal model delta sigma weight residual 110.28 123.15 -12.87 1.48e+00 4.57e-01 7.56e+01 angle pdb=" N PHE C 375 " pdb=" CA PHE C 375 " pdb=" C PHE C 375 " ideal model delta sigma weight residual 110.28 123.14 -12.86 1.48e+00 4.57e-01 7.55e+01 angle pdb=" N PHE B 375 " pdb=" CA PHE B 375 " pdb=" C PHE B 375 " ideal model delta sigma weight residual 110.28 123.12 -12.84 1.48e+00 4.57e-01 7.53e+01 angle pdb=" N ILE A 794 " pdb=" CA ILE A 794 " pdb=" C ILE A 794 " ideal model delta sigma weight residual 110.05 103.16 6.89 1.09e+00 8.42e-01 3.99e+01 angle pdb=" C THR C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 120.31 114.31 6.00 9.80e-01 1.04e+00 3.75e+01 ... (remaining 41615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 18164 17.67 - 35.34: 704 35.34 - 53.02: 175 53.02 - 70.69: 61 70.69 - 88.36: 28 Dihedral angle restraints: 19132 sinusoidal: 8398 harmonic: 10734 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.74 -69.26 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.70 -62.30 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.52 46.52 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 19129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4837 0.330 - 0.660: 6 0.660 - 0.990: 6 0.990 - 1.321: 3 1.321 - 1.651: 1 Chirality restraints: 4853 Sorted by residual: chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.52e+03 chirality pdb=" C1 NAG A1407 " pdb=" O4 NAG A1406 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.52e+03 chirality pdb=" C1 NAG B1407 " pdb=" O4 NAG B1406 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.50e+03 ... (remaining 4850 not shown) Planarity restraints: 5337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.252 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" CG ASN C 331 " -0.104 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.480 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.372 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.197 2.00e-02 2.50e+03 2.43e-01 7.41e+02 pdb=" CG ASN A 343 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " 0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.197 2.00e-02 2.50e+03 2.43e-01 7.40e+02 pdb=" CG ASN C 343 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG C1406 " 0.281 2.00e-02 2.50e+03 ... (remaining 5334 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 102 2.53 - 3.12: 22539 3.12 - 3.71: 42510 3.71 - 4.31: 65103 4.31 - 4.90: 105803 Nonbonded interactions: 236057 Sorted by model distance: nonbonded pdb=" O ARG A 328 " pdb=" CD1 PHE A 329 " model vdw 1.933 3.340 nonbonded pdb=" O ASN B 334 " pdb=" O VAL B 362 " model vdw 2.210 3.040 nonbonded pdb=" CG PRO B 521 " pdb=" OH TYR C 200 " model vdw 2.233 3.440 nonbonded pdb=" O GLY H 104 " pdb=" N CYS H 106 " model vdw 2.238 3.120 nonbonded pdb=" O GLY K 104 " pdb=" N CYS K 106 " model vdw 2.238 3.120 ... (remaining 236052 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 939 or resid 944 through 1146 or resid 1401 thr \ ough 1410)) selection = (chain 'B' and (resid 27 through 1146 or resid 1401 through 1410)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 1.310 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: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.610 Set scattering table: 0.280 Process input model: 68.110 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 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 : 0.010 0.232 30738 Z= 0.586 Angle : 1.427 48.957 41929 Z= 0.781 Chirality : 0.080 1.651 4853 Planarity : 0.007 0.098 5289 Dihedral : 10.860 88.361 12104 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 1.84 % Allowed : 5.64 % Favored : 92.52 % Rotamer: Outliers : 1.40 % Allowed : 2.46 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.13), residues: 3634 helix: -1.27 (0.17), residues: 676 sheet: -0.43 (0.15), residues: 966 loop : -1.85 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.130 0.012 TRP H 53 HIS 0.006 0.001 HIS E 95 PHE 0.034 0.002 PHE K 29 TYR 0.070 0.004 TYR L 36 ARG 0.007 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.04573 ( 48) link_NAG-ASN : angle 8.44113 ( 144) link_BETA1-4 : bond 0.06777 ( 23) link_BETA1-4 : angle 11.54640 ( 69) hydrogen bonds : bond 0.20544 ( 1116) hydrogen bonds : angle 8.57384 ( 3117) SS BOND : bond 0.08732 ( 48) SS BOND : angle 11.18266 ( 96) covalent geometry : bond 0.00949 (30619) covalent geometry : angle 1.13861 (41620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 452 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7706 (mm) cc_final: 0.7504 (tp) REVERT: B 408 ARG cc_start: 0.1885 (OUTLIER) cc_final: 0.1149 (ptm160) REVERT: B 569 ILE cc_start: 0.8825 (tt) cc_final: 0.8520 (tt) outliers start: 45 outliers final: 13 residues processed: 497 average time/residue: 0.4222 time to fit residues: 330.4552 Evaluate side-chains 220 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 5.9990 chunk 275 optimal weight: 0.0970 chunk 152 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 329 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS A 239 GLN A 388 ASN A 544 ASN B 52 GLN B 239 GLN B 388 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 321 GLN C 388 ASN C 690 GLN C 907 ASN C 913 GLN C 992 GLN C1010 GLN K 82 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.206636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141953 restraints weight = 54308.027| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 5.09 r_work: 0.3558 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30738 Z= 0.205 Angle : 0.816 15.381 41929 Z= 0.401 Chirality : 0.051 0.421 4853 Planarity : 0.006 0.062 5289 Dihedral : 5.936 58.960 5512 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.87 % Favored : 94.91 % Rotamer: Outliers : 2.49 % Allowed : 6.45 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3634 helix: 0.24 (0.20), residues: 662 sheet: -0.56 (0.15), residues: 985 loop : -1.35 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 53 HIS 0.006 0.001 HIS A1064 PHE 0.037 0.002 PHE B 823 TYR 0.027 0.002 TYR B 369 ARG 0.009 0.001 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.01180 ( 48) link_NAG-ASN : angle 3.30332 ( 144) link_BETA1-4 : bond 0.00921 ( 23) link_BETA1-4 : angle 2.58198 ( 69) hydrogen bonds : bond 0.05003 ( 1116) hydrogen bonds : angle 6.04931 ( 3117) SS BOND : bond 0.00779 ( 48) SS BOND : angle 3.07774 ( 96) covalent geometry : bond 0.00463 (30619) covalent geometry : angle 0.77503 (41620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 219 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6711 (mpp) cc_final: 0.5259 (tpt) REVERT: A 207 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6697 (m90) REVERT: A 654 GLU cc_start: 0.8377 (tt0) cc_final: 0.8102 (tp30) REVERT: A 787 GLN cc_start: 0.8563 (mp10) cc_final: 0.8341 (mp10) REVERT: A 820 ASP cc_start: 0.8610 (t70) cc_final: 0.8370 (t0) REVERT: A 1002 GLN cc_start: 0.7669 (mm110) cc_final: 0.7440 (mm110) REVERT: B 58 PHE cc_start: 0.7827 (m-10) cc_final: 0.7564 (m-80) REVERT: B 332 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5718 (mp) REVERT: B 376 THR cc_start: 0.2274 (OUTLIER) cc_final: 0.1884 (p) REVERT: B 407 VAL cc_start: 0.1194 (OUTLIER) cc_final: 0.0815 (m) REVERT: B 755 GLN cc_start: 0.8630 (mm110) cc_final: 0.7649 (pt0) REVERT: B 902 MET cc_start: 0.8628 (tpt) cc_final: 0.8342 (tpt) REVERT: B 955 ASN cc_start: 0.8247 (m-40) cc_final: 0.7958 (m-40) REVERT: C 204 TYR cc_start: 0.7700 (m-80) cc_final: 0.7307 (m-80) REVERT: C 725 GLU cc_start: 0.7665 (tt0) cc_final: 0.7429 (tt0) REVERT: L 33 LEU cc_start: 0.4194 (tt) cc_final: 0.3918 (tp) REVERT: L 98 THR cc_start: 0.3517 (m) cc_final: 0.2901 (p) outliers start: 80 outliers final: 41 residues processed: 287 average time/residue: 0.3869 time to fit residues: 182.6461 Evaluate side-chains 210 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 191 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 237 optimal weight: 0.2980 chunk 296 optimal weight: 1.9990 chunk 329 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 272 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 345 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 30 ASN B 544 ASN B 907 ASN B 913 GLN C 690 GLN C 762 GLN C 907 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.206605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140909 restraints weight = 54470.322| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 4.90 r_work: 0.3555 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30738 Z= 0.117 Angle : 0.654 14.989 41929 Z= 0.319 Chirality : 0.046 0.385 4853 Planarity : 0.004 0.046 5289 Dihedral : 5.285 56.904 5497 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.38 % Favored : 95.40 % Rotamer: Outliers : 2.18 % Allowed : 7.61 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 3634 helix: 0.86 (0.20), residues: 676 sheet: -0.14 (0.16), residues: 934 loop : -1.15 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 53 HIS 0.003 0.001 HIS A 207 PHE 0.022 0.001 PHE C 329 TYR 0.019 0.001 TYR H 107 ARG 0.006 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 48) link_NAG-ASN : angle 2.78004 ( 144) link_BETA1-4 : bond 0.00686 ( 23) link_BETA1-4 : angle 2.16228 ( 69) hydrogen bonds : bond 0.04111 ( 1116) hydrogen bonds : angle 5.58079 ( 3117) SS BOND : bond 0.00545 ( 48) SS BOND : angle 2.52133 ( 96) covalent geometry : bond 0.00255 (30619) covalent geometry : angle 0.61776 (41620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 187 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6637 (mpp) cc_final: 0.5831 (ttp) REVERT: A 207 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.5962 (m-70) REVERT: A 654 GLU cc_start: 0.8361 (tt0) cc_final: 0.8110 (tp30) REVERT: A 787 GLN cc_start: 0.8554 (mp10) cc_final: 0.8189 (mp10) REVERT: A 820 ASP cc_start: 0.8542 (t70) cc_final: 0.8160 (t0) REVERT: B 755 GLN cc_start: 0.8665 (mm110) cc_final: 0.7766 (pt0) REVERT: B 781 VAL cc_start: 0.8996 (t) cc_final: 0.8774 (t) REVERT: C 204 TYR cc_start: 0.7806 (m-80) cc_final: 0.6849 (m-80) REVERT: C 725 GLU cc_start: 0.7684 (tt0) cc_final: 0.7449 (tt0) REVERT: C 959 LEU cc_start: 0.8838 (mt) cc_final: 0.8511 (tp) REVERT: E 105 ASP cc_start: -0.2569 (OUTLIER) cc_final: -0.2884 (m-30) REVERT: H 102 CYS cc_start: 0.2876 (OUTLIER) cc_final: 0.2164 (t) outliers start: 70 outliers final: 36 residues processed: 250 average time/residue: 0.3696 time to fit residues: 156.0032 Evaluate side-chains 201 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 252 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 161 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 762 GLN C 907 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.202596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133579 restraints weight = 54026.420| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.98 r_work: 0.3406 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 30738 Z= 0.152 Angle : 0.649 10.310 41929 Z= 0.318 Chirality : 0.046 0.361 4853 Planarity : 0.005 0.050 5289 Dihedral : 5.145 41.652 5489 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.87 % Favored : 94.94 % Rotamer: Outliers : 2.18 % Allowed : 7.92 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3634 helix: 1.09 (0.21), residues: 661 sheet: -0.25 (0.16), residues: 976 loop : -1.02 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 53 HIS 0.019 0.001 HIS A 207 PHE 0.022 0.002 PHE C 329 TYR 0.018 0.001 TYR A1067 ARG 0.008 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 48) link_NAG-ASN : angle 2.54435 ( 144) link_BETA1-4 : bond 0.00613 ( 23) link_BETA1-4 : angle 1.99656 ( 69) hydrogen bonds : bond 0.04064 ( 1116) hydrogen bonds : angle 5.36007 ( 3117) SS BOND : bond 0.00794 ( 48) SS BOND : angle 2.37500 ( 96) covalent geometry : bond 0.00356 (30619) covalent geometry : angle 0.61783 (41620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6741 (mpp) cc_final: 0.5924 (ttp) REVERT: A 197 ILE cc_start: 0.8417 (mm) cc_final: 0.8215 (tp) REVERT: A 377 PHE cc_start: 0.3999 (OUTLIER) cc_final: 0.3638 (m-80) REVERT: A 787 GLN cc_start: 0.8632 (mp10) cc_final: 0.8323 (mp10) REVERT: A 820 ASP cc_start: 0.8599 (t70) cc_final: 0.8240 (t0) REVERT: A 1029 MET cc_start: 0.9056 (tpp) cc_final: 0.8756 (tpp) REVERT: B 755 GLN cc_start: 0.8679 (mm110) cc_final: 0.7963 (pt0) REVERT: C 204 TYR cc_start: 0.7975 (m-80) cc_final: 0.6906 (m-80) REVERT: C 725 GLU cc_start: 0.7930 (tt0) cc_final: 0.7677 (tt0) REVERT: E 105 ASP cc_start: -0.2800 (OUTLIER) cc_final: -0.3114 (m-30) outliers start: 70 outliers final: 44 residues processed: 233 average time/residue: 0.3464 time to fit residues: 138.6993 Evaluate side-chains 201 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 73 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 328 optimal weight: 7.9990 chunk 236 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 130 optimal weight: 0.0770 chunk 344 optimal weight: 5.9990 chunk 321 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 207 HIS A 245 HIS A 271 GLN A 762 GLN A 901 GLN B 907 ASN C 690 GLN C 762 GLN C 907 ASN C1071 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.197995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124374 restraints weight = 53284.731| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 4.41 r_work: 0.3336 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30738 Z= 0.210 Angle : 0.692 10.452 41929 Z= 0.345 Chirality : 0.048 0.341 4853 Planarity : 0.005 0.079 5289 Dihedral : 5.499 46.353 5489 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.75 % Favored : 94.06 % Rotamer: Outliers : 2.31 % Allowed : 8.76 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 3634 helix: 0.90 (0.20), residues: 656 sheet: -0.40 (0.16), residues: 964 loop : -1.05 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 53 HIS 0.007 0.001 HIS B1058 PHE 0.027 0.002 PHE C 275 TYR 0.021 0.002 TYR H 101 ARG 0.009 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 48) link_NAG-ASN : angle 2.52420 ( 144) link_BETA1-4 : bond 0.00778 ( 23) link_BETA1-4 : angle 1.94044 ( 69) hydrogen bonds : bond 0.04603 ( 1116) hydrogen bonds : angle 5.49031 ( 3117) SS BOND : bond 0.00511 ( 48) SS BOND : angle 2.44049 ( 96) covalent geometry : bond 0.00502 (30619) covalent geometry : angle 0.66385 (41620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 170 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6827 (mpp) cc_final: 0.6076 (ttp) REVERT: A 197 ILE cc_start: 0.8449 (mm) cc_final: 0.8240 (tp) REVERT: A 377 PHE cc_start: 0.4125 (OUTLIER) cc_final: 0.3733 (m-80) REVERT: A 787 GLN cc_start: 0.8998 (mp10) cc_final: 0.8600 (mp10) REVERT: A 820 ASP cc_start: 0.8604 (t70) cc_final: 0.8313 (t0) REVERT: A 1092 GLU cc_start: 0.7825 (pm20) cc_final: 0.7548 (tm-30) REVERT: B 287 ASP cc_start: 0.8231 (t0) cc_final: 0.7537 (m-30) REVERT: B 580 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: B 755 GLN cc_start: 0.8691 (mm110) cc_final: 0.7960 (pt0) REVERT: B 950 ASP cc_start: 0.7840 (m-30) cc_final: 0.7631 (t0) REVERT: B 1092 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7607 (mm-30) REVERT: C 204 TYR cc_start: 0.8028 (m-80) cc_final: 0.7818 (m-80) REVERT: C 725 GLU cc_start: 0.8024 (tt0) cc_final: 0.7749 (tt0) REVERT: C 959 LEU cc_start: 0.8880 (mt) cc_final: 0.8677 (tp) REVERT: L 4 MET cc_start: 0.2552 (ttt) cc_final: 0.1717 (tpp) REVERT: L 33 LEU cc_start: 0.4308 (tp) cc_final: 0.3977 (tp) outliers start: 74 outliers final: 50 residues processed: 234 average time/residue: 0.3826 time to fit residues: 150.1914 Evaluate side-chains 190 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 192 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 335 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 358 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 252 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 690 GLN A 762 GLN A 901 GLN A1088 HIS C 675 GLN C 690 GLN C 762 GLN C 907 ASN I 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.195766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123044 restraints weight = 53350.616| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.68 r_work: 0.3351 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 30738 Z= 0.249 Angle : 0.718 12.241 41929 Z= 0.358 Chirality : 0.049 0.340 4853 Planarity : 0.005 0.057 5289 Dihedral : 5.877 49.149 5489 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.14 % Favored : 93.70 % Rotamer: Outliers : 2.40 % Allowed : 9.82 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3634 helix: 0.75 (0.20), residues: 653 sheet: -0.37 (0.17), residues: 913 loop : -1.16 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 104 HIS 0.007 0.001 HIS B1048 PHE 0.027 0.002 PHE A 86 TYR 0.021 0.002 TYR A1067 ARG 0.005 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 48) link_NAG-ASN : angle 2.52231 ( 144) link_BETA1-4 : bond 0.00618 ( 23) link_BETA1-4 : angle 1.88906 ( 69) hydrogen bonds : bond 0.04790 ( 1116) hydrogen bonds : angle 5.50623 ( 3117) SS BOND : bond 0.00458 ( 48) SS BOND : angle 2.59479 ( 96) covalent geometry : bond 0.00601 (30619) covalent geometry : angle 0.69018 (41620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 157 time to evaluate : 3.496 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6565 (m-90) cc_final: 0.6128 (m-90) REVERT: A 197 ILE cc_start: 0.8563 (mm) cc_final: 0.8344 (tp) REVERT: A 207 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6401 (m-70) REVERT: A 377 PHE cc_start: 0.3919 (OUTLIER) cc_final: 0.3404 (m-80) REVERT: A 787 GLN cc_start: 0.9038 (mp10) cc_final: 0.8742 (mp10) REVERT: A 820 ASP cc_start: 0.8588 (t70) cc_final: 0.8129 (m-30) REVERT: A 1029 MET cc_start: 0.9054 (tpp) cc_final: 0.8754 (tpp) REVERT: B 200 TYR cc_start: 0.7471 (m-80) cc_final: 0.7249 (m-80) REVERT: B 578 ASP cc_start: 0.7075 (t70) cc_final: 0.6863 (t0) REVERT: B 580 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: B 586 ASP cc_start: 0.7327 (m-30) cc_final: 0.6814 (t0) REVERT: B 755 GLN cc_start: 0.8705 (mm110) cc_final: 0.7986 (pt0) REVERT: C 204 TYR cc_start: 0.8337 (m-80) cc_final: 0.8107 (m-80) REVERT: C 725 GLU cc_start: 0.7993 (tt0) cc_final: 0.7696 (tt0) REVERT: L 4 MET cc_start: 0.2354 (ttt) cc_final: 0.1787 (tpp) outliers start: 77 outliers final: 56 residues processed: 218 average time/residue: 0.4030 time to fit residues: 152.2996 Evaluate side-chains 202 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 187 optimal weight: 0.5980 chunk 221 optimal weight: 0.8980 chunk 297 optimal weight: 30.0000 chunk 222 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 141 optimal weight: 50.0000 chunk 97 optimal weight: 2.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 580 GLN C 690 GLN C 762 GLN C 907 ASN I 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.196593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.124464 restraints weight = 53246.452| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 4.72 r_work: 0.3319 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30738 Z= 0.175 Angle : 0.651 10.063 41929 Z= 0.322 Chirality : 0.046 0.331 4853 Planarity : 0.005 0.048 5289 Dihedral : 5.693 53.514 5489 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.25 % Rotamer: Outliers : 2.00 % Allowed : 10.47 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3634 helix: 0.97 (0.20), residues: 656 sheet: -0.40 (0.17), residues: 917 loop : -1.11 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.029 0.001 HIS A 207 PHE 0.023 0.002 PHE B 429 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 48) link_NAG-ASN : angle 2.34536 ( 144) link_BETA1-4 : bond 0.00575 ( 23) link_BETA1-4 : angle 1.82072 ( 69) hydrogen bonds : bond 0.04242 ( 1116) hydrogen bonds : angle 5.35852 ( 3117) SS BOND : bond 0.00457 ( 48) SS BOND : angle 2.31987 ( 96) covalent geometry : bond 0.00423 (30619) covalent geometry : angle 0.62446 (41620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6382 (m-90) cc_final: 0.5305 (m-90) REVERT: A 377 PHE cc_start: 0.3872 (OUTLIER) cc_final: 0.3373 (m-80) REVERT: A 787 GLN cc_start: 0.9037 (mp10) cc_final: 0.8522 (mp10) REVERT: A 820 ASP cc_start: 0.8527 (t70) cc_final: 0.8130 (m-30) REVERT: A 1029 MET cc_start: 0.9034 (tpp) cc_final: 0.8759 (tpp) REVERT: B 755 GLN cc_start: 0.8683 (mm110) cc_final: 0.7950 (pt0) REVERT: B 1050 MET cc_start: 0.8323 (ptm) cc_final: 0.8057 (ptp) REVERT: C 725 GLU cc_start: 0.8030 (tt0) cc_final: 0.7729 (tt0) REVERT: K 34 MET cc_start: 0.1112 (ptp) cc_final: 0.0861 (ptp) REVERT: L 4 MET cc_start: 0.2427 (ttt) cc_final: 0.1851 (tpp) outliers start: 64 outliers final: 49 residues processed: 206 average time/residue: 0.3353 time to fit residues: 121.0100 Evaluate side-chains 189 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 210 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 331 optimal weight: 40.0000 chunk 211 optimal weight: 0.9990 chunk 347 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 224 optimal weight: 30.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 762 GLN C 239 GLN C 690 GLN C 762 GLN C 907 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.196277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123837 restraints weight = 53662.794| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 4.74 r_work: 0.3358 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30738 Z= 0.171 Angle : 0.647 10.433 41929 Z= 0.320 Chirality : 0.046 0.324 4853 Planarity : 0.005 0.052 5289 Dihedral : 5.629 57.932 5489 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.11 % Rotamer: Outliers : 2.00 % Allowed : 10.66 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3634 helix: 1.08 (0.21), residues: 655 sheet: -0.41 (0.17), residues: 941 loop : -1.05 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.029 0.001 HIS A 207 PHE 0.022 0.002 PHE A 86 TYR 0.029 0.001 TYR C 904 ARG 0.007 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 48) link_NAG-ASN : angle 2.28287 ( 144) link_BETA1-4 : bond 0.00584 ( 23) link_BETA1-4 : angle 1.80558 ( 69) hydrogen bonds : bond 0.04137 ( 1116) hydrogen bonds : angle 5.27799 ( 3117) SS BOND : bond 0.00371 ( 48) SS BOND : angle 2.33670 ( 96) covalent geometry : bond 0.00413 (30619) covalent geometry : angle 0.62083 (41620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 145 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6417 (m-90) cc_final: 0.6129 (m-90) REVERT: A 153 MET cc_start: 0.6542 (mpp) cc_final: 0.5924 (tmm) REVERT: A 207 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.6227 (m-70) REVERT: A 377 PHE cc_start: 0.4081 (OUTLIER) cc_final: 0.3581 (m-80) REVERT: A 787 GLN cc_start: 0.9050 (mp10) cc_final: 0.8726 (mp10) REVERT: A 820 ASP cc_start: 0.8460 (t70) cc_final: 0.8106 (m-30) REVERT: B 755 GLN cc_start: 0.8672 (mm110) cc_final: 0.7941 (pt0) REVERT: B 1050 MET cc_start: 0.8287 (ptm) cc_final: 0.8083 (ptp) REVERT: C 237 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7361 (mtp-110) REVERT: C 725 GLU cc_start: 0.7976 (tt0) cc_final: 0.7692 (tt0) REVERT: K 34 MET cc_start: 0.1110 (ptp) cc_final: 0.0894 (ptp) REVERT: L 4 MET cc_start: 0.2539 (ttt) cc_final: 0.1907 (tpp) outliers start: 64 outliers final: 51 residues processed: 199 average time/residue: 0.3565 time to fit residues: 123.6451 Evaluate side-chains 194 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 82 optimal weight: 8.9990 chunk 256 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 305 optimal weight: 50.0000 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 chunk 296 optimal weight: 1.9990 chunk 353 optimal weight: 40.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 762 GLN B 188 ASN C 690 GLN C 762 GLN C 907 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.194620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122342 restraints weight = 53288.425| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 4.78 r_work: 0.3303 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 30738 Z= 0.227 Angle : 0.697 15.343 41929 Z= 0.345 Chirality : 0.047 0.323 4853 Planarity : 0.005 0.060 5289 Dihedral : 5.783 50.710 5489 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.25 % Favored : 93.59 % Rotamer: Outliers : 2.06 % Allowed : 10.79 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3634 helix: 0.96 (0.20), residues: 655 sheet: -0.53 (0.16), residues: 977 loop : -1.10 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 64 HIS 0.026 0.001 HIS A 207 PHE 0.025 0.002 PHE A 86 TYR 0.021 0.002 TYR A1067 ARG 0.010 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 48) link_NAG-ASN : angle 2.34724 ( 144) link_BETA1-4 : bond 0.00580 ( 23) link_BETA1-4 : angle 1.82199 ( 69) hydrogen bonds : bond 0.04591 ( 1116) hydrogen bonds : angle 5.40935 ( 3117) SS BOND : bond 0.00459 ( 48) SS BOND : angle 2.58666 ( 96) covalent geometry : bond 0.00553 (30619) covalent geometry : angle 0.67077 (41620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 141 time to evaluate : 3.049 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6484 (m-90) cc_final: 0.6250 (m-90) REVERT: A 197 ILE cc_start: 0.8503 (mm) cc_final: 0.8240 (tp) REVERT: A 377 PHE cc_start: 0.3902 (OUTLIER) cc_final: 0.3479 (m-80) REVERT: A 787 GLN cc_start: 0.9072 (mp10) cc_final: 0.8764 (mp10) REVERT: A 820 ASP cc_start: 0.8543 (t70) cc_final: 0.8185 (m-30) REVERT: A 1029 MET cc_start: 0.9082 (tpp) cc_final: 0.8857 (ttm) REVERT: B 586 ASP cc_start: 0.7314 (m-30) cc_final: 0.6724 (t0) REVERT: B 661 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 755 GLN cc_start: 0.8700 (mm110) cc_final: 0.7945 (pt0) REVERT: C 158 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.5061 (ptt90) REVERT: C 725 GLU cc_start: 0.8011 (tt0) cc_final: 0.7713 (tt0) REVERT: C 1144 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7475 (mt-10) REVERT: K 34 MET cc_start: 0.1172 (ptp) cc_final: 0.0954 (ptp) REVERT: L 4 MET cc_start: 0.3409 (ttt) cc_final: 0.2814 (tpp) outliers start: 66 outliers final: 54 residues processed: 199 average time/residue: 0.3553 time to fit residues: 121.3867 Evaluate side-chains 193 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 319 optimal weight: 30.0000 chunk 214 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 321 optimal weight: 40.0000 chunk 352 optimal weight: 30.0000 chunk 76 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 83 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1054 GLN C 690 GLN C 762 GLN C 907 ASN C1054 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.194710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.120932 restraints weight = 53833.372| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.60 r_work: 0.3328 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30738 Z= 0.112 Angle : 0.621 15.343 41929 Z= 0.306 Chirality : 0.045 0.317 4853 Planarity : 0.004 0.064 5289 Dihedral : 5.467 45.162 5489 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 1.22 % Allowed : 11.63 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3634 helix: 1.34 (0.21), residues: 655 sheet: -0.34 (0.16), residues: 965 loop : -0.96 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 53 HIS 0.019 0.001 HIS A 207 PHE 0.021 0.001 PHE B 86 TYR 0.019 0.001 TYR C1067 ARG 0.009 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 48) link_NAG-ASN : angle 2.17346 ( 144) link_BETA1-4 : bond 0.00621 ( 23) link_BETA1-4 : angle 1.77630 ( 69) hydrogen bonds : bond 0.03693 ( 1116) hydrogen bonds : angle 5.20431 ( 3117) SS BOND : bond 0.00331 ( 48) SS BOND : angle 2.18691 ( 96) covalent geometry : bond 0.00257 (30619) covalent geometry : angle 0.59701 (41620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 3.035 Fit side-chains REVERT: A 197 ILE cc_start: 0.8447 (mm) cc_final: 0.8209 (tp) REVERT: A 207 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6334 (m-70) REVERT: A 377 PHE cc_start: 0.4237 (OUTLIER) cc_final: 0.3770 (m-80) REVERT: A 787 GLN cc_start: 0.9009 (mp10) cc_final: 0.8641 (mp10) REVERT: A 820 ASP cc_start: 0.8368 (t70) cc_final: 0.8074 (m-30) REVERT: B 200 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: B 755 GLN cc_start: 0.8648 (mm110) cc_final: 0.7900 (pt0) REVERT: C 158 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.5046 (ptt90) REVERT: C 725 GLU cc_start: 0.7896 (tt0) cc_final: 0.7604 (tt0) REVERT: L 4 MET cc_start: 0.2969 (ttt) cc_final: 0.2270 (tpp) outliers start: 39 outliers final: 30 residues processed: 179 average time/residue: 0.3750 time to fit residues: 114.5212 Evaluate side-chains 173 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0968 > 50: distance: 40 - 149: 28.970 distance: 59 - 78: 30.749 distance: 74 - 78: 27.994 distance: 78 - 79: 27.698 distance: 79 - 80: 19.124 distance: 79 - 82: 65.064 distance: 80 - 81: 16.966 distance: 80 - 87: 43.550 distance: 82 - 83: 38.407 distance: 83 - 84: 41.334 distance: 84 - 85: 4.468 distance: 84 - 86: 27.225 distance: 87 - 88: 56.340 distance: 88 - 89: 70.054 distance: 88 - 91: 38.494 distance: 89 - 90: 46.468 distance: 89 - 95: 68.108 distance: 92 - 93: 41.382 distance: 92 - 94: 59.207 distance: 95 - 96: 69.766 distance: 96 - 97: 38.998 distance: 96 - 99: 56.738 distance: 97 - 98: 40.785 distance: 100 - 101: 18.578 distance: 100 - 102: 39.232 distance: 103 - 104: 68.785 distance: 104 - 105: 15.323 distance: 104 - 107: 56.436 distance: 105 - 106: 62.905 distance: 105 - 113: 26.702 distance: 107 - 108: 56.961 distance: 108 - 109: 38.764 distance: 108 - 110: 57.323 distance: 109 - 111: 70.585 distance: 110 - 112: 57.419 distance: 111 - 112: 55.579 distance: 114 - 115: 25.165 distance: 114 - 117: 40.241 distance: 115 - 116: 48.426 distance: 115 - 118: 27.435 distance: 118 - 119: 39.516 distance: 118 - 124: 54.109 distance: 119 - 120: 38.550 distance: 119 - 122: 55.919 distance: 120 - 121: 56.399 distance: 122 - 123: 40.251 distance: 123 - 124: 57.350 distance: 126 - 127: 69.522 distance: 126 - 129: 41.387 distance: 127 - 128: 40.617 distance: 130 - 131: 5.966 distance: 131 - 132: 35.564 distance: 131 - 134: 47.571 distance: 132 - 133: 56.251 distance: 134 - 135: 45.788 distance: 134 - 136: 46.360 distance: 137 - 138: 39.490 distance: 138 - 139: 39.663 distance: 138 - 141: 54.811 distance: 139 - 144: 56.413 distance: 141 - 142: 57.478 distance: 141 - 143: 30.021 distance: 145 - 146: 52.375 distance: 145 - 148: 41.302 distance: 146 - 147: 35.323 distance: 146 - 150: 31.866 distance: 148 - 149: 27.289