Starting phenix.real_space_refine on Fri Jun 27 23:19:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ls9_23506/06_2025/7ls9_23506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ls9_23506/06_2025/7ls9_23506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ls9_23506/06_2025/7ls9_23506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ls9_23506/06_2025/7ls9_23506.map" model { file = "/net/cci-nas-00/data/ceres_data/7ls9_23506/06_2025/7ls9_23506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ls9_23506/06_2025/7ls9_23506.cif" } resolution = 3.42 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= 0.003 sd= 0.021 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 144 5.16 5 C 20436 2.51 5 N 5304 2.21 5 O 6342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32226 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "E" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "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: "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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "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: "A" 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 Chain: "B" 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 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: 17.71, per 1000 atoms: 0.55 Number of scatterers: 32226 At special positions: 0 Unit cell: (140.17, 140.17, 206.51, 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 144 16.00 O 6342 8.00 N 5304 7.00 C 20436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100F" distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100A" - pdb=" SG CYS D 100F" distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 100A" - pdb=" SG CYS E 100F" distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 17 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 17 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 17 " " NAG C1310 " - " ASN C 343 " " NAG I 1 " - " ASN A 165 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN B 165 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN C 165 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN A 717 " " NAG a 1 " - " ASN A 801 " " NAG b 1 " - " ASN A1098 " " NAG c 1 " - " ASN A1134 " " NAG d 1 " - " ASN A 122 " Time building additional restraints: 8.11 Conformation dependent library (CDL) restraints added in 3.9 seconds 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7446 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 69 sheets defined 22.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.040A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.306A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 832 through 838 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.929A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.970A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.254A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.713A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.846A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.215A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.871A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.766A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 31 removed outlier: 4.248A pdb=" N SER L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.090A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.050A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.300A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.650A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.161A 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 502 through 506 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.626A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 749 through 757 Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.782A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 889 removed outlier: 3.702A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 889' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.100A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.618A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.822A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.006A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.900A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 52A through 54 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.900A pdb=" N THR D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 removed outlier: 3.906A pdb=" N SER F 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.077A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.882A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.296A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.737A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.285A 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 502 through 506 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.601A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 749 through 783 removed outlier: 6.415A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 832 through 838 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.810A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.236A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.174A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.642A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.806A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.287A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.801A pdb=" N THR E 87 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 31 removed outlier: 4.202A pdb=" N SER G 31 " --> pdb=" O VAL G 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 31' Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.155A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.083A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.814A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.519A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.891A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.616A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.230A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.791A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.755A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.647A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.647A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 100 through 100B Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.511A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.511A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.124A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.806A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.819A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 141 through 144 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.008A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.008A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.192A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.719A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.175A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.512A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.733A pdb=" N THR D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.733A pdb=" N THR D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 100 through 100B removed outlier: 3.522A pdb=" N ILE D 100B" --> pdb=" O VAL D 100E" (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.587A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.608A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN F 37 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.608A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.810A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.787A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 141 through 144 Processing sheet with id=AF7, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.038A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.038A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.750A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.684A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.684A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.794A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1098 Processing sheet with id=AG9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AH1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.912A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.912A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 100 through 100B Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.593A pdb=" N SER G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.674A pdb=" N GLN G 89 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 37 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.699A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.07 Time building geometry restraints manager: 9.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5373 1.32 - 1.46: 11551 1.46 - 1.59: 15840 1.59 - 1.73: 2 1.73 - 1.86: 180 Bond restraints: 32946 Sorted by residual: bond pdb=" CG PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 1.503 1.244 0.259 3.40e-02 8.65e+02 5.79e+01 bond pdb=" CG PRO G 59 " pdb=" CD PRO G 59 " ideal model delta sigma weight residual 1.503 1.309 0.194 3.40e-02 8.65e+02 3.26e+01 bond pdb=" CA ALA D 99 " pdb=" CB ALA D 99 " ideal model delta sigma weight residual 1.530 1.463 0.066 1.48e-02 4.57e+03 2.01e+01 bond pdb=" CA ALA H 99 " pdb=" CB ALA H 99 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.66e-02 3.63e+03 1.61e+01 bond pdb=" C PHE E 100G" pdb=" O PHE E 100G" ideal model delta sigma weight residual 1.236 1.189 0.046 1.17e-02 7.31e+03 1.58e+01 ... (remaining 32941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 44321 3.29 - 6.58: 435 6.58 - 9.88: 50 9.88 - 13.17: 4 13.17 - 16.46: 4 Bond angle restraints: 44814 Sorted by residual: angle pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 112.00 95.54 16.46 1.40e+00 5.10e-01 1.38e+02 angle pdb=" N PRO F 40 " pdb=" CD PRO F 40 " pdb=" CG PRO F 40 " ideal model delta sigma weight residual 103.20 87.93 15.27 1.50e+00 4.44e-01 1.04e+02 angle pdb=" CA GLY C 447 " pdb=" C GLY C 447 " pdb=" O GLY C 447 " ideal model delta sigma weight residual 121.88 114.92 6.96 7.80e-01 1.64e+00 7.97e+01 angle pdb=" N PRO G 59 " pdb=" CD PRO G 59 " pdb=" CG PRO G 59 " ideal model delta sigma weight residual 103.20 90.02 13.18 1.50e+00 4.44e-01 7.72e+01 angle pdb=" C PHE A 140 " pdb=" CA PHE A 140 " pdb=" CB PHE A 140 " ideal model delta sigma weight residual 111.17 95.96 15.21 1.96e+00 2.60e-01 6.02e+01 ... (remaining 44809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 19383 21.66 - 43.32: 1006 43.32 - 64.98: 116 64.98 - 86.64: 45 86.64 - 108.30: 15 Dihedral angle restraints: 20565 sinusoidal: 8949 harmonic: 11616 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.51 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.81 -76.19 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.44 -75.56 1 1.00e+01 1.00e-02 7.21e+01 ... (remaining 20562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4792 0.096 - 0.192: 416 0.192 - 0.288: 44 0.288 - 0.384: 3 0.384 - 0.479: 4 Chirality restraints: 5259 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.33e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.10e+01 ... (remaining 5256 not shown) Planarity restraints: 5751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.244 2.00e-02 2.50e+03 2.07e-01 5.37e+02 pdb=" C7 NAG I 2 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.342 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.232 2.00e-02 2.50e+03 1.97e-01 4.86e+02 pdb=" C7 NAG K 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.323 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " -0.221 2.00e-02 2.50e+03 1.88e-01 4.42e+02 pdb=" C7 NAG P 2 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " 0.308 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " -0.171 2.00e-02 2.50e+03 ... (remaining 5748 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5085 2.77 - 3.30: 28806 3.30 - 3.83: 52493 3.83 - 4.37: 59924 4.37 - 4.90: 106489 Nonbonded interactions: 252797 Sorted by model distance: nonbonded pdb=" OG SER B 494 " pdb=" OH TYR F 32 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLN B 314 " pdb=" OG SER C 735 " model vdw 2.282 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.315 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.331 3.040 ... (remaining 252792 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.230 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 74.720 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 33075 Z= 0.288 Angle : 0.900 16.459 45147 Z= 0.521 Chirality : 0.057 0.479 5259 Planarity : 0.008 0.207 5700 Dihedral : 12.843 108.299 12957 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.17 % 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: -0.75 (0.12), residues: 3954 helix: -0.05 (0.18), residues: 741 sheet: 0.48 (0.17), residues: 963 loop : -1.11 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 35 HIS 0.012 0.001 HIS B 519 PHE 0.043 0.002 PHE C 817 TYR 0.035 0.002 TYR B 741 ARG 0.017 0.001 ARG G 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 51) link_NAG-ASN : angle 2.18990 ( 153) link_BETA1-4 : bond 0.00589 ( 24) link_BETA1-4 : angle 1.74236 ( 72) hydrogen bonds : bond 0.21728 ( 1235) hydrogen bonds : angle 8.67611 ( 3528) SS BOND : bond 0.00599 ( 54) SS BOND : angle 1.48435 ( 108) covalent geometry : bond 0.00543 (32946) covalent geometry : angle 0.88817 (44814) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 3.453 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 725 GLU cc_start: 0.7602 (pp20) cc_final: 0.7284 (pp20) REVERT: A 864 LEU cc_start: 0.7503 (tp) cc_final: 0.7124 (tp) REVERT: H 4 LEU cc_start: 0.8613 (mm) cc_final: 0.8249 (mm) REVERT: H 57 THR cc_start: 0.8853 (p) cc_final: 0.8553 (m) REVERT: L 53 SER cc_start: 0.7978 (t) cc_final: 0.7589 (p) REVERT: B 406 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6757 (mm-30) REVERT: D 4 LEU cc_start: 0.8327 (mm) cc_final: 0.7838 (mm) REVERT: F 2 ILE cc_start: 0.8290 (mp) cc_final: 0.8030 (mp) REVERT: F 27 GLN cc_start: 0.7368 (pt0) cc_final: 0.6528 (pp30) REVERT: F 53 SER cc_start: 0.8263 (t) cc_final: 0.7734 (p) REVERT: F 54 ARG cc_start: 0.7958 (mpt90) cc_final: 0.7534 (mtt90) REVERT: E 4 LEU cc_start: 0.8408 (mm) cc_final: 0.8157 (mm) REVERT: E 101 ASP cc_start: 0.8075 (t0) cc_final: 0.7806 (t0) REVERT: G 49 TYR cc_start: 0.8182 (p90) cc_final: 0.7799 (p90) REVERT: G 53 SER cc_start: 0.7441 (t) cc_final: 0.7027 (t) REVERT: G 79 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7196 (pm20) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.4403 time to fit residues: 312.6277 Evaluate side-chains 312 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 0.4980 chunk 297 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 498 GLN A 519 HIS A 613 GLN A 644 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 498 GLN B 519 HIS B 613 GLN B 644 GLN B1011 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 519 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.128978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100358 restraints weight = 66682.579| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.12 r_work: 0.3522 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33075 Z= 0.151 Angle : 0.604 10.340 45147 Z= 0.309 Chirality : 0.044 0.170 5259 Planarity : 0.004 0.061 5700 Dihedral : 6.281 64.759 5895 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.72 % Allowed : 7.53 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.26 (0.13), residues: 3954 helix: 0.84 (0.19), residues: 744 sheet: 0.50 (0.16), residues: 1056 loop : -0.89 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 35 HIS 0.004 0.001 HIS D 32 PHE 0.021 0.001 PHE A 140 TYR 0.023 0.001 TYR B1067 ARG 0.005 0.000 ARG F 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 51) link_NAG-ASN : angle 1.36302 ( 153) link_BETA1-4 : bond 0.00327 ( 24) link_BETA1-4 : angle 1.66891 ( 72) hydrogen bonds : bond 0.04804 ( 1235) hydrogen bonds : angle 6.30108 ( 3528) SS BOND : bond 0.00341 ( 54) SS BOND : angle 1.03346 ( 108) covalent geometry : bond 0.00341 (32946) covalent geometry : angle 0.59481 (44814) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 346 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7139 (p0) cc_final: 0.6856 (p0) REVERT: A 864 LEU cc_start: 0.8544 (tp) cc_final: 0.8326 (tp) REVERT: A 1005 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7370 (tm-30) REVERT: H 107 THR cc_start: 0.7854 (p) cc_final: 0.7549 (t) REVERT: L 77 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8372 (ttp80) REVERT: B 131 CYS cc_start: 0.6626 (m) cc_final: 0.6370 (m) REVERT: B 869 MET cc_start: 0.8706 (mtm) cc_final: 0.8457 (ttm) REVERT: D 58 GLU cc_start: 0.8085 (mp0) cc_final: 0.7798 (mp0) REVERT: F 2 ILE cc_start: 0.8531 (mp) cc_final: 0.8114 (mp) REVERT: F 27 GLN cc_start: 0.8255 (pt0) cc_final: 0.7527 (pp30) REVERT: F 53 SER cc_start: 0.7721 (t) cc_final: 0.7360 (p) REVERT: F 62 PHE cc_start: 0.6832 (m-80) cc_final: 0.6627 (m-80) REVERT: F 77 ARG cc_start: 0.8673 (ttp-110) cc_final: 0.8362 (ttp-110) REVERT: C 389 ASP cc_start: 0.6412 (p0) cc_final: 0.5974 (p0) REVERT: C 390 LEU cc_start: 0.7507 (mt) cc_final: 0.7283 (mt) REVERT: C 740 MET cc_start: 0.8786 (mmm) cc_final: 0.8481 (tpt) REVERT: C 965 GLN cc_start: 0.8094 (tp40) cc_final: 0.7518 (mm110) REVERT: C 1005 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7470 (tm-30) REVERT: E 81 GLN cc_start: 0.8192 (tp40) cc_final: 0.7978 (tp40) REVERT: E 101 ASP cc_start: 0.8324 (t0) cc_final: 0.7984 (t0) REVERT: G 77 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.8059 (ttp80) outliers start: 25 outliers final: 17 residues processed: 364 average time/residue: 0.4506 time to fit residues: 260.3544 Evaluate side-chains 314 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 297 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 68.0374 > 50: distance: 21 - 29: 18.970 distance: 29 - 30: 10.538 distance: 29 - 161: 17.517 distance: 30 - 31: 9.507 distance: 30 - 33: 14.681 distance: 31 - 32: 12.340 distance: 31 - 38: 14.734 distance: 32 - 158: 23.142 distance: 33 - 34: 15.776 distance: 34 - 35: 8.201 distance: 35 - 36: 14.932 distance: 36 - 37: 14.484 distance: 38 - 39: 4.925 distance: 39 - 40: 9.173 distance: 39 - 42: 6.300 distance: 40 - 41: 8.645 distance: 40 - 44: 32.966 distance: 42 - 43: 11.430 distance: 43 - 157: 14.446 distance: 44 - 45: 10.060 distance: 44 - 151: 19.681 distance: 45 - 46: 10.332 distance: 45 - 48: 5.975 distance: 46 - 47: 8.755 distance: 46 - 56: 15.816 distance: 47 - 148: 26.049 distance: 48 - 49: 9.101 distance: 49 - 50: 5.943 distance: 49 - 51: 4.541 distance: 50 - 52: 9.399 distance: 51 - 53: 9.363 distance: 52 - 54: 5.422 distance: 53 - 54: 7.461 distance: 54 - 55: 7.055 distance: 56 - 57: 27.858 distance: 57 - 58: 35.018 distance: 58 - 59: 32.508 distance: 58 - 60: 40.028 distance: 60 - 61: 27.430 distance: 61 - 62: 18.038 distance: 61 - 64: 14.848 distance: 62 - 63: 22.533 distance: 62 - 67: 23.896 distance: 64 - 65: 23.299 distance: 64 - 66: 3.834 distance: 67 - 68: 26.756 distance: 68 - 69: 23.439 distance: 68 - 71: 32.652 distance: 69 - 70: 29.370 distance: 69 - 73: 17.570 distance: 71 - 72: 23.827 distance: 73 - 74: 27.963 distance: 73 - 79: 37.394 distance: 74 - 75: 32.940 distance: 74 - 77: 31.428 distance: 75 - 76: 13.342 distance: 75 - 80: 15.035 distance: 76 - 96: 7.568 distance: 77 - 78: 22.878 distance: 78 - 79: 40.753 distance: 80 - 81: 22.320 distance: 81 - 82: 22.677 distance: 81 - 84: 18.389 distance: 82 - 83: 20.397 distance: 82 - 87: 29.262 distance: 84 - 85: 25.531 distance: 84 - 86: 13.886 distance: 87 - 88: 28.385 distance: 88 - 89: 36.512 distance: 88 - 91: 21.061 distance: 89 - 90: 5.864 distance: 89 - 96: 18.519 distance: 91 - 92: 11.554 distance: 92 - 93: 11.866 distance: 93 - 94: 19.197 distance: 96 - 97: 5.589 distance: 97 - 98: 9.569 distance: 97 - 100: 13.171 distance: 98 - 99: 9.397 distance: 98 - 104: 6.050 distance: 100 - 101: 9.680 distance: 101 - 102: 12.074