Starting phenix.real_space_refine on Sat May 17 12:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dua_27718/05_2025/8dua_27718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dua_27718/05_2025/8dua_27718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dua_27718/05_2025/8dua_27718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dua_27718/05_2025/8dua_27718.map" model { file = "/net/cci-nas-00/data/ceres_data/8dua_27718/05_2025/8dua_27718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dua_27718/05_2025/8dua_27718.cif" } resolution = 4.32 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= 0.002 sd= 0.015 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 84 5.16 5 C 9804 2.51 5 N 2520 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15612 Number of models: 1 Model: "" Number of chains: 33 Chain: "B" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 762 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "G" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2354 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 3 Chain: "H" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 888 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 762 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "C" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2354 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 3 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 888 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "E" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "F" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 762 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "I" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2354 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 3 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 888 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" 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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" 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: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" 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: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 9.35, per 1000 atoms: 0.60 Number of scatterers: 15612 At special positions: 0 Unit cell: (138.624, 133.209, 116.964, 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 84 16.00 O 3204 8.00 N 2520 7.00 C 9804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 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 Atom "HETATM15358 O5 NAG G1008 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 701 " - " ASN A 625 " " NAG B 701 " - " ASN B 625 " " NAG C1001 " - " ASN C 290 " " NAG C1002 " - " ASN C 268 " " NAG C1003 " - " ASN C 279 " " NAG C1004 " - " ASN C 446 " " NAG C1005 " - " ASN C 354 " " NAG C1006 " - " ASN C 88 " " NAG C1007 " - " ASN C 97 " " NAG C1008 " - " ASN C 238 " " NAG F 701 " - " ASN F 625 " " NAG G1001 " - " ASN G 290 " " NAG G1002 " - " ASN G 268 " " NAG G1003 " - " ASN G 446 " " NAG G1004 " - " ASN G 354 " " NAG G1005 " - " ASN G 88 " " NAG G1006 " - " ASN G 97 " " NAG G1007 " - " ASN G 238 " " NAG G1008 " - " ASN G 279 " " NAG I1001 " - " ASN I 290 " " NAG I1002 " - " ASN I 268 " " NAG I1003 " - " ASN I 446 " " NAG I1004 " - " ASN I 354 " " NAG I1005 " - " ASN I 88 " " NAG I1006 " - " ASN I 97 " " NAG I1007 " - " ASN I 238 " " NAG I1008 " - " ASN I 279 " " NAG M 1 " - " ASN B 641 " " NAG N 1 " - " ASN B 612 " " NAG O 1 " - " ASN G 229 " " NAG P 1 " - " ASN G 262 " " NAG Q 1 " - " ASN G 47 " " NAG R 1 " - " ASN A 641 " " NAG S 1 " - " ASN A 612 " " NAG T 1 " - " ASN C 229 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 47 " " NAG W 1 " - " ASN F 641 " " NAG X 1 " - " ASN F 612 " " NAG Y 1 " - " ASN I 229 " " NAG Z 1 " - " ASN I 262 " " NAG a 1 " - " ASN I 47 " Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 1.8 seconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 31 sheets defined 22.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'B' and resid 570 through 593 removed outlier: 3.825A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.883A pdb=" N ARG B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 664 removed outlier: 4.374A pdb=" N ALA B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 645 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU B 647 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU B 648 " --> pdb=" O GLN B 644 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS B 662 " --> pdb=" O TYR B 658 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 removed outlier: 4.422A pdb=" N GLN G 73 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.980A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN G 103 " --> pdb=" O THR G 99 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA G 104 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 removed outlier: 3.627A pdb=" N GLU G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU G 347 " --> pdb=" O GLN G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.518A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 removed outlier: 4.153A pdb=" N LEU G 391 " --> pdb=" O MET G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 483 removed outlier: 4.186A pdb=" N TYR G 479 " --> pdb=" O VAL G 475 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 480 " --> pdb=" O ALA G 476 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU G 482 " --> pdb=" O LEU G 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 571 through 593 removed outlier: 3.812A pdb=" N GLN A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.902A pdb=" N ARG A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 664 removed outlier: 4.380A pdb=" N ALA A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 645 " --> pdb=" O ASN A 641 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU A 647 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 648 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 662 " --> pdb=" O TYR A 658 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 4.425A pdb=" N GLN C 73 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.992A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.676A pdb=" N GLU C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.520A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 removed outlier: 4.112A pdb=" N LEU C 391 " --> pdb=" O MET C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.189A pdb=" N TYR C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C 482 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'F' and resid 571 through 593 removed outlier: 3.805A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 620 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.904A pdb=" N ARG F 633 " --> pdb=" O GLN F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 664 removed outlier: 4.375A pdb=" N ALA F 640 " --> pdb=" O ASP F 636 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASN F 641 " --> pdb=" O PHE F 637 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN F 644 " --> pdb=" O ALA F 640 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 645 " --> pdb=" O ASN F 641 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU F 647 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU F 648 " --> pdb=" O GLN F 644 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN F 661 " --> pdb=" O MET F 657 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS F 662 " --> pdb=" O TYR F 658 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU F 663 " --> pdb=" O GLU F 659 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 removed outlier: 4.416A pdb=" N GLN I 73 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 3.993A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN I 103 " --> pdb=" O THR I 99 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA I 104 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 352 removed outlier: 3.642A pdb=" N GLU I 344 " --> pdb=" O GLU I 340 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU I 347 " --> pdb=" O GLN I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.528A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.105A pdb=" N LEU I 391 " --> pdb=" O MET I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 483 removed outlier: 4.184A pdb=" N TYR I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG I 480 " --> pdb=" O ALA I 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU I 482 " --> pdb=" O LEU I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.821A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.513A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 242 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL G 244 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 84 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 272 through 274 removed outlier: 3.787A pdb=" N ILE G 282 " --> pdb=" O TYR G 273 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP G 457 " --> pdb=" O ASN G 465 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN G 465 " --> pdb=" O ASP G 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 293 through 296 removed outlier: 3.568A pdb=" N MET G 294 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.134A pdb=" N GLN H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.648A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.011A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.524A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 44 through 49 removed outlier: 6.017A pdb=" N ARG L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.830A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.511A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 242 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 244 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 84 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 272 through 274 removed outlier: 3.750A pdb=" N ILE C 282 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 281 " --> pdb=" O ALA C 454 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 454 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 293 through 296 removed outlier: 3.585A pdb=" N MET C 294 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 456 through 457 removed outlier: 4.009A pdb=" N ASP C 457 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 465 " --> pdb=" O ASP C 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 5 through 7 removed outlier: 4.125A pdb=" N GLN D 5 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 82 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 20 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.271A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG D 38 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.271A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG D 38 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.911A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.534A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 63 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 49 removed outlier: 6.050A pdb=" N ARG E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN E 37 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.820A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.509A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL I 242 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL I 244 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU I 84 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 272 through 274 removed outlier: 3.716A pdb=" N ILE I 282 " --> pdb=" O TYR I 273 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 293 through 296 removed outlier: 3.597A pdb=" N MET I 294 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 456 through 457 removed outlier: 3.992A pdb=" N ASP I 457 " --> pdb=" O ASN I 465 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN I 465 " --> pdb=" O ASP I 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'J' and resid 5 through 7 removed outlier: 4.127A pdb=" N GLN J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU J 20 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 46 through 47 removed outlier: 4.254A pdb=" N GLU J 46 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 46 through 47 removed outlier: 4.254A pdb=" N GLU J 46 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.998A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.523A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER K 63 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 44 through 49 removed outlier: 6.018A pdb=" N ARG K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN K 37 " --> pdb=" O ARG K 46 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 927 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: 3.89 Time building geometry restraints manager: 5.37 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: 2539 1.33 - 1.45: 4799 1.45 - 1.58: 8520 1.58 - 1.70: 0 1.70 - 1.83: 111 Bond restraints: 15969 Sorted by residual: bond pdb=" CA ASN G 279 " pdb=" C ASN G 279 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.22e-02 6.72e+03 1.74e+01 bond pdb=" N ARG C 280 " pdb=" CA ARG C 280 " ideal model delta sigma weight residual 1.455 1.500 -0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" N ILE C 282 " pdb=" CA ILE C 282 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.19e-02 7.06e+03 8.80e+00 bond pdb=" N ARG I 280 " pdb=" CA ARG I 280 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.21e+00 bond pdb=" N ASN C 279 " pdb=" CA ASN C 279 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.99e+00 ... (remaining 15964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 21137 2.19 - 4.38: 452 4.38 - 6.57: 130 6.57 - 8.76: 10 8.76 - 10.95: 3 Bond angle restraints: 21732 Sorted by residual: angle pdb=" CA ASN G 279 " pdb=" CB ASN G 279 " pdb=" CG ASN G 279 " ideal model delta sigma weight residual 112.60 101.82 10.78 1.00e+00 1.00e+00 1.16e+02 angle pdb=" N ASN C 279 " pdb=" CA ASN C 279 " pdb=" C ASN C 279 " ideal model delta sigma weight residual 112.72 103.07 9.65 1.14e+00 7.69e-01 7.16e+01 angle pdb=" N ASN I 279 " pdb=" CA ASN I 279 " pdb=" C ASN I 279 " ideal model delta sigma weight residual 112.23 103.86 8.37 1.26e+00 6.30e-01 4.41e+01 angle pdb=" C ASN I 279 " pdb=" CA ASN I 279 " pdb=" CB ASN I 279 " ideal model delta sigma weight residual 110.38 121.33 -10.95 2.04e+00 2.40e-01 2.88e+01 angle pdb=" N THR C 281 " pdb=" CA THR C 281 " pdb=" C THR C 281 " ideal model delta sigma weight residual 109.14 116.65 -7.51 1.49e+00 4.50e-01 2.54e+01 ... (remaining 21727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 9690 24.04 - 48.07: 592 48.07 - 72.11: 110 72.11 - 96.14: 90 96.14 - 120.18: 63 Dihedral angle restraints: 10545 sinusoidal: 5274 harmonic: 5271 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 147.67 -54.67 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual -86.00 -31.80 -54.20 1 1.00e+01 1.00e-02 3.98e+01 ... (remaining 10542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 2585 0.142 - 0.284: 45 0.284 - 0.426: 12 0.426 - 0.568: 0 0.568 - 0.710: 1 Chirality restraints: 2643 Sorted by residual: chirality pdb=" C1 NAG I1008 " pdb=" ND2 ASN I 279 " pdb=" C2 NAG I1008 " pdb=" O5 NAG I1008 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA GLU C 347 " pdb=" N GLU C 347 " pdb=" C GLU C 347 " pdb=" CB GLU C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA GLU I 347 " pdb=" N GLU I 347 " pdb=" C GLU I 347 " pdb=" CB GLU I 347 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 2640 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I1008 " 0.183 2.00e-02 2.50e+03 1.49e-01 2.79e+02 pdb=" C7 NAG I1008 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG I1008 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG I1008 " -0.239 2.00e-02 2.50e+03 pdb=" O7 NAG I1008 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 277 " -0.025 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C LYS G 277 " 0.088 2.00e-02 2.50e+03 pdb=" O LYS G 277 " -0.034 2.00e-02 2.50e+03 pdb=" N SER G 278 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G1008 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG G1008 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G1008 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G1008 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG G1008 " 0.008 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 115 2.49 - 3.09: 11278 3.09 - 3.70: 20916 3.70 - 4.30: 29338 4.30 - 4.90: 47766 Nonbonded interactions: 109413 Sorted by model distance: nonbonded pdb=" O3 NAG C1003 " pdb=" O7 NAG C1003 " model vdw 1.889 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.114 3.040 nonbonded pdb=" OD1 ASN A 612 " pdb=" OG1 THR A 614 " model vdw 2.119 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.131 3.040 nonbonded pdb=" OD1 ASN B 612 " pdb=" OG1 THR B 614 " model vdw 2.133 3.040 ... (remaining 109408 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 34.380 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 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 0.095 16083 Z= 0.250 Angle : 0.904 50.222 22047 Z= 0.398 Chirality : 0.058 0.710 2643 Planarity : 0.004 0.149 2619 Dihedral : 19.514 120.178 7074 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.25 % Rotamer: Outliers : 0.19 % Allowed : 0.25 % Favored : 99.56 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % 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: -1.65 (0.19), residues: 1773 helix: -0.84 (0.32), residues: 240 sheet: 0.35 (0.34), residues: 234 loop : -1.54 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 458 HIS 0.009 0.001 HIS C 352 PHE 0.005 0.001 PHE I 53 TYR 0.007 0.001 TYR C 352C ARG 0.002 0.000 ARG C 249 Details of bonding type rmsd link_NAG-ASN : bond 0.01570 ( 42) link_NAG-ASN : angle 5.66998 ( 126) link_ALPHA1-6 : bond 0.00469 ( 6) link_ALPHA1-6 : angle 1.57227 ( 18) link_BETA1-4 : bond 0.00482 ( 30) link_BETA1-4 : angle 1.88975 ( 90) link_ALPHA1-3 : bond 0.00586 ( 9) link_ALPHA1-3 : angle 2.16250 ( 27) hydrogen bonds : bond 0.34490 ( 345) hydrogen bonds : angle 9.72353 ( 927) SS BOND : bond 0.00216 ( 27) SS BOND : angle 0.56683 ( 54) covalent geometry : bond 0.00476 (15969) covalent geometry : angle 0.78733 (21732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 255 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 THR cc_start: 0.4464 (p) cc_final: 0.3095 (p) REVERT: H 72 ASP cc_start: 0.6744 (p0) cc_final: 0.6482 (p0) REVERT: L 54 LEU cc_start: 0.8139 (tp) cc_final: 0.7675 (tt) REVERT: A 576 LEU cc_start: 0.8280 (mm) cc_final: 0.7919 (mm) REVERT: A 645 LEU cc_start: 0.8485 (mm) cc_final: 0.8238 (mm) REVERT: D 58 THR cc_start: 0.5844 (p) cc_final: 0.5317 (p) REVERT: E 94 ASP cc_start: 0.6691 (t0) cc_final: 0.6279 (t70) REVERT: J 86 ASP cc_start: 0.7213 (m-30) cc_final: 0.6966 (m-30) outliers start: 3 outliers final: 3 residues processed: 258 average time/residue: 0.3352 time to fit residues: 119.5685 Evaluate side-chains 135 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 160 optimal weight: 0.0040 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN G 377 ASN A 661 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN F 594 ASN F 661 GLN I 254 GLN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.051250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.041436 restraints weight = 169219.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.042268 restraints weight = 123438.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.042876 restraints weight = 100203.951| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16083 Z= 0.183 Angle : 0.837 10.442 22047 Z= 0.384 Chirality : 0.052 0.400 2643 Planarity : 0.005 0.107 2619 Dihedral : 15.718 112.799 3738 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.95 % Rotamer: Outliers : 0.38 % Allowed : 3.26 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.19), residues: 1773 helix: -0.38 (0.30), residues: 267 sheet: 0.57 (0.31), residues: 267 loop : -1.64 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 109 HIS 0.002 0.001 HIS G 352 PHE 0.030 0.002 PHE A 600 TYR 0.036 0.002 TYR J 90 ARG 0.011 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 42) link_NAG-ASN : angle 3.22960 ( 126) link_ALPHA1-6 : bond 0.00970 ( 6) link_ALPHA1-6 : angle 1.94976 ( 18) link_BETA1-4 : bond 0.00469 ( 30) link_BETA1-4 : angle 2.61898 ( 90) link_ALPHA1-3 : bond 0.00870 ( 9) link_ALPHA1-3 : angle 3.64110 ( 27) hydrogen bonds : bond 0.05521 ( 345) hydrogen bonds : angle 7.37073 ( 927) SS BOND : bond 0.00386 ( 27) SS BOND : angle 0.82279 ( 54) covalent geometry : bond 0.00388 (15969) covalent geometry : angle 0.77525 (21732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 1.668 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: B 577 GLN cc_start: 0.9527 (tt0) cc_final: 0.9085 (tp-100) REVERT: B 639 GLU cc_start: 0.9160 (pp20) cc_final: 0.8907 (pp20) REVERT: B 652 GLN cc_start: 0.9703 (tt0) cc_final: 0.9369 (tm-30) REVERT: G 250 MET cc_start: 0.9153 (mmp) cc_final: 0.8415 (tpp) REVERT: G 468 MET cc_start: 0.3154 (ttp) cc_final: 0.2286 (pmm) REVERT: H 72 ASP cc_start: 0.8614 (p0) cc_final: 0.8300 (p0) REVERT: A 652 GLN cc_start: 0.9704 (tt0) cc_final: 0.9303 (tm-30) REVERT: C 468 MET cc_start: 0.3811 (tmm) cc_final: 0.3497 (tmm) REVERT: D 58 THR cc_start: 0.8709 (p) cc_final: 0.8273 (t) REVERT: D 60 TYR cc_start: 0.8789 (m-10) cc_final: 0.8368 (m-80) REVERT: F 639 GLU cc_start: 0.8974 (pp20) cc_final: 0.8753 (pp20) REVERT: I 479 TYR cc_start: 0.8548 (m-80) cc_final: 0.8272 (m-80) REVERT: J 86 ASP cc_start: 0.7969 (m-30) cc_final: 0.7648 (m-30) REVERT: J 90 TYR cc_start: 0.8835 (m-80) cc_final: 0.8379 (m-80) REVERT: J 107 LEU cc_start: 0.9211 (tp) cc_final: 0.8997 (tp) REVERT: K 30 ASP cc_start: 0.9391 (t70) cc_final: 0.8774 (t0) outliers start: 6 outliers final: 0 residues processed: 169 average time/residue: 0.2845 time to fit residues: 69.6916 Evaluate side-chains 118 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 0.0050 chunk 62 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 592 GLN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.049488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.039741 restraints weight = 167965.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.040591 restraints weight = 122265.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.041178 restraints weight = 98661.265| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16083 Z= 0.157 Angle : 0.744 10.818 22047 Z= 0.339 Chirality : 0.050 0.339 2643 Planarity : 0.004 0.065 2619 Dihedral : 12.563 114.209 3738 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.25 % Allowed : 2.76 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.18), residues: 1773 helix: -0.33 (0.29), residues: 273 sheet: 0.33 (0.27), residues: 291 loop : -1.72 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 610 HIS 0.001 0.000 HIS I 275 PHE 0.013 0.001 PHE B 600 TYR 0.019 0.001 TYR B 586 ARG 0.011 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 42) link_NAG-ASN : angle 2.91380 ( 126) link_ALPHA1-6 : bond 0.01541 ( 6) link_ALPHA1-6 : angle 3.56927 ( 18) link_BETA1-4 : bond 0.00494 ( 30) link_BETA1-4 : angle 2.30782 ( 90) link_ALPHA1-3 : bond 0.01101 ( 9) link_ALPHA1-3 : angle 2.68066 ( 27) hydrogen bonds : bond 0.04813 ( 345) hydrogen bonds : angle 6.49631 ( 927) SS BOND : bond 0.00381 ( 27) SS BOND : angle 0.67662 ( 54) covalent geometry : bond 0.00331 (15969) covalent geometry : angle 0.68494 (21732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 583 ILE cc_start: 0.9759 (OUTLIER) cc_final: 0.9457 (tp) REVERT: B 584 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9146 (pp20) REVERT: B 588 LYS cc_start: 0.9719 (tmtt) cc_final: 0.9504 (tptp) REVERT: B 652 GLN cc_start: 0.9687 (tt0) cc_final: 0.9406 (tm-30) REVERT: G 250 MET cc_start: 0.9229 (mmp) cc_final: 0.8541 (tpp) REVERT: G 468 MET cc_start: 0.4383 (tmm) cc_final: 0.3657 (tmm) REVERT: H 60 TYR cc_start: 0.8852 (m-80) cc_final: 0.8637 (m-80) REVERT: H 72 ASP cc_start: 0.8554 (p0) cc_final: 0.8246 (p0) REVERT: A 652 GLN cc_start: 0.9646 (tt0) cc_final: 0.9277 (tm-30) REVERT: C 250 MET cc_start: 0.9256 (mmm) cc_final: 0.8684 (tpp) REVERT: C 468 MET cc_start: 0.3833 (tmm) cc_final: 0.3389 (tmm) REVERT: D 58 THR cc_start: 0.8835 (p) cc_final: 0.7655 (p) REVERT: F 639 GLU cc_start: 0.9032 (pp20) cc_final: 0.8709 (pp20) REVERT: J 86 ASP cc_start: 0.7977 (m-30) cc_final: 0.7582 (m-30) REVERT: J 90 TYR cc_start: 0.8748 (m-80) cc_final: 0.8294 (m-80) REVERT: J 107 LEU cc_start: 0.9210 (tp) cc_final: 0.8992 (tp) REVERT: K 30 ASP cc_start: 0.9347 (t70) cc_final: 0.8713 (t0) outliers start: 4 outliers final: 0 residues processed: 145 average time/residue: 0.2829 time to fit residues: 61.1008 Evaluate side-chains 112 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 150 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.0020 chunk 68 optimal weight: 0.2980 chunk 111 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.049903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.040094 restraints weight = 165222.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.040996 restraints weight = 118574.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.041623 restraints weight = 94983.459| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16083 Z= 0.120 Angle : 0.718 10.138 22047 Z= 0.322 Chirality : 0.050 0.402 2643 Planarity : 0.004 0.036 2619 Dihedral : 11.398 112.900 3738 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.25 % Allowed : 2.45 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.19), residues: 1773 helix: -0.17 (0.30), residues: 273 sheet: 0.51 (0.29), residues: 279 loop : -1.60 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 33 HIS 0.002 0.000 HIS G 352 PHE 0.013 0.001 PHE B 600 TYR 0.011 0.001 TYR C 35 ARG 0.007 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 42) link_NAG-ASN : angle 2.83608 ( 126) link_ALPHA1-6 : bond 0.01414 ( 6) link_ALPHA1-6 : angle 2.45387 ( 18) link_BETA1-4 : bond 0.00476 ( 30) link_BETA1-4 : angle 2.20054 ( 90) link_ALPHA1-3 : bond 0.01133 ( 9) link_ALPHA1-3 : angle 3.03075 ( 27) hydrogen bonds : bond 0.04046 ( 345) hydrogen bonds : angle 6.12996 ( 927) SS BOND : bond 0.00236 ( 27) SS BOND : angle 0.70017 ( 54) covalent geometry : bond 0.00243 (15969) covalent geometry : angle 0.66219 (21732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 588 LYS cc_start: 0.9725 (tmtt) cc_final: 0.9474 (tptp) REVERT: B 639 GLU cc_start: 0.9140 (pp20) cc_final: 0.8854 (pp20) REVERT: B 652 GLN cc_start: 0.9675 (tt0) cc_final: 0.9402 (tm-30) REVERT: G 250 MET cc_start: 0.9239 (mmp) cc_final: 0.8571 (tpp) REVERT: G 468 MET cc_start: 0.4457 (tmm) cc_final: 0.4012 (tmm) REVERT: H 60 TYR cc_start: 0.8905 (m-80) cc_final: 0.8656 (m-80) REVERT: H 72 ASP cc_start: 0.8607 (p0) cc_final: 0.8360 (p0) REVERT: A 648 GLU cc_start: 0.9600 (mp0) cc_final: 0.9307 (pm20) REVERT: A 652 GLN cc_start: 0.9647 (tt0) cc_final: 0.9214 (tm-30) REVERT: C 250 MET cc_start: 0.9299 (mmm) cc_final: 0.8661 (tpp) REVERT: C 468 MET cc_start: 0.4073 (tmm) cc_final: 0.3546 (tmm) REVERT: F 574 LYS cc_start: 0.9411 (tptp) cc_final: 0.9152 (tptp) REVERT: F 639 GLU cc_start: 0.9122 (pp20) cc_final: 0.8803 (pp20) REVERT: J 86 ASP cc_start: 0.7920 (m-30) cc_final: 0.7558 (m-30) REVERT: J 90 TYR cc_start: 0.8747 (m-80) cc_final: 0.8447 (m-80) REVERT: J 107 LEU cc_start: 0.9239 (tp) cc_final: 0.9009 (tp) REVERT: K 30 ASP cc_start: 0.9384 (t70) cc_final: 0.8758 (t0) outliers start: 4 outliers final: 0 residues processed: 151 average time/residue: 0.2770 time to fit residues: 62.9352 Evaluate side-chains 117 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 13 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 112 optimal weight: 0.0970 chunk 70 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 GLN H 82AASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.043239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.034028 restraints weight = 186508.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.034835 restraints weight = 130451.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.035391 restraints weight = 103802.251| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 16083 Z= 0.292 Angle : 0.923 10.008 22047 Z= 0.441 Chirality : 0.053 0.440 2643 Planarity : 0.006 0.077 2619 Dihedral : 10.003 110.958 3738 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.25 % Allowed : 4.14 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.18), residues: 1773 helix: -0.50 (0.27), residues: 291 sheet: -0.43 (0.26), residues: 330 loop : -1.99 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP F 610 HIS 0.004 0.002 HIS L 55 PHE 0.021 0.003 PHE C 259 TYR 0.037 0.003 TYR B 586 ARG 0.018 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 42) link_NAG-ASN : angle 3.03176 ( 126) link_ALPHA1-6 : bond 0.01748 ( 6) link_ALPHA1-6 : angle 2.70410 ( 18) link_BETA1-4 : bond 0.00557 ( 30) link_BETA1-4 : angle 2.29561 ( 90) link_ALPHA1-3 : bond 0.01097 ( 9) link_ALPHA1-3 : angle 2.83505 ( 27) hydrogen bonds : bond 0.04470 ( 345) hydrogen bonds : angle 6.68823 ( 927) SS BOND : bond 0.00403 ( 27) SS BOND : angle 1.22137 ( 54) covalent geometry : bond 0.00612 (15969) covalent geometry : angle 0.87694 (21732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9539 (tptp) cc_final: 0.9198 (tptt) REVERT: B 588 LYS cc_start: 0.9792 (tmtt) cc_final: 0.9569 (tptp) REVERT: B 639 GLU cc_start: 0.9240 (pp20) cc_final: 0.9022 (pp20) REVERT: B 652 GLN cc_start: 0.9691 (tt0) cc_final: 0.9426 (tm-30) REVERT: G 250 MET cc_start: 0.9229 (mmp) cc_final: 0.8827 (tpp) REVERT: G 468 MET cc_start: 0.6080 (tmm) cc_final: 0.5424 (ppp) REVERT: H 60 TYR cc_start: 0.8943 (m-80) cc_final: 0.8708 (m-10) REVERT: A 583 ILE cc_start: 0.9774 (OUTLIER) cc_final: 0.9558 (tp) REVERT: A 652 GLN cc_start: 0.9724 (tt0) cc_final: 0.9386 (tm-30) REVERT: C 468 MET cc_start: 0.5847 (tmm) cc_final: 0.5022 (ppp) REVERT: F 574 LYS cc_start: 0.9453 (tptp) cc_final: 0.9103 (tptp) REVERT: F 583 ILE cc_start: 0.9739 (OUTLIER) cc_final: 0.9407 (tp) REVERT: F 639 GLU cc_start: 0.9232 (pp20) cc_final: 0.8970 (pp20) REVERT: I 374 MET cc_start: 0.5814 (pmm) cc_final: 0.5395 (pmm) REVERT: J 3 GLN cc_start: 0.8614 (pm20) cc_final: 0.8084 (mp10) REVERT: J 107 LEU cc_start: 0.9295 (tp) cc_final: 0.9052 (tp) REVERT: K 70 LYS cc_start: 0.9359 (tptt) cc_final: 0.9155 (tptp) outliers start: 4 outliers final: 0 residues processed: 121 average time/residue: 0.2684 time to fit residues: 49.6657 Evaluate side-chains 97 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 60 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 45 optimal weight: 0.4980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 254 GLN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.043961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.034701 restraints weight = 177185.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035493 restraints weight = 126304.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.036031 restraints weight = 101709.423| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16083 Z= 0.153 Angle : 0.762 10.646 22047 Z= 0.348 Chirality : 0.050 0.346 2643 Planarity : 0.004 0.034 2619 Dihedral : 9.618 110.349 3738 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.85 (0.19), residues: 1773 helix: -0.26 (0.27), residues: 291 sheet: -0.55 (0.26), residues: 354 loop : -1.81 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 610 HIS 0.002 0.001 HIS C 275 PHE 0.021 0.002 PHE A 637 TYR 0.019 0.001 TYR B 658 ARG 0.009 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 42) link_NAG-ASN : angle 3.07595 ( 126) link_ALPHA1-6 : bond 0.01780 ( 6) link_ALPHA1-6 : angle 3.23960 ( 18) link_BETA1-4 : bond 0.00365 ( 30) link_BETA1-4 : angle 2.12762 ( 90) link_ALPHA1-3 : bond 0.00947 ( 9) link_ALPHA1-3 : angle 2.84373 ( 27) hydrogen bonds : bond 0.03811 ( 345) hydrogen bonds : angle 6.22391 ( 927) SS BOND : bond 0.00465 ( 27) SS BOND : angle 0.76046 ( 54) covalent geometry : bond 0.00317 (15969) covalent geometry : angle 0.70410 (21732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.668 Fit side-chains revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9575 (tptp) cc_final: 0.9218 (tptp) REVERT: B 588 LYS cc_start: 0.9800 (tmtt) cc_final: 0.9565 (tptp) REVERT: B 639 GLU cc_start: 0.9277 (pp20) cc_final: 0.9036 (pp20) REVERT: B 652 GLN cc_start: 0.9704 (tt0) cc_final: 0.9431 (tm-30) REVERT: G 250 MET cc_start: 0.9257 (mmp) cc_final: 0.8793 (tpp) REVERT: G 468 MET cc_start: 0.6252 (tmm) cc_final: 0.5619 (ppp) REVERT: H 60 TYR cc_start: 0.9005 (m-80) cc_final: 0.8753 (m-10) REVERT: L 30 ASP cc_start: 0.9441 (t0) cc_final: 0.9188 (t0) REVERT: A 652 GLN cc_start: 0.9726 (tt0) cc_final: 0.9389 (tm-30) REVERT: C 250 MET cc_start: 0.9381 (mmp) cc_final: 0.8853 (tpp) REVERT: C 468 MET cc_start: 0.6045 (tmm) cc_final: 0.5500 (ppp) REVERT: E 4 MET cc_start: 0.7573 (mmp) cc_final: 0.7122 (mmm) REVERT: F 574 LYS cc_start: 0.9518 (tptp) cc_final: 0.9146 (tptp) REVERT: F 588 LYS cc_start: 0.9754 (tmtt) cc_final: 0.9529 (tptp) REVERT: F 639 GLU cc_start: 0.9235 (pp20) cc_final: 0.8940 (pp20) REVERT: I 468 MET cc_start: 0.3515 (tmm) cc_final: 0.3226 (tmm) REVERT: J 107 LEU cc_start: 0.9257 (tp) cc_final: 0.9013 (tp) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2896 time to fit residues: 54.3395 Evaluate side-chains 91 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 35 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.041378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.032489 restraints weight = 187104.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.033263 restraints weight = 132159.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.033795 restraints weight = 105806.497| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16083 Z= 0.240 Angle : 0.844 9.482 22047 Z= 0.394 Chirality : 0.050 0.444 2643 Planarity : 0.005 0.059 2619 Dihedral : 9.325 107.233 3738 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.19), residues: 1773 helix: -0.01 (0.28), residues: 291 sheet: -0.98 (0.25), residues: 390 loop : -1.96 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 610 HIS 0.004 0.001 HIS L 55 PHE 0.019 0.002 PHE L 62 TYR 0.033 0.002 TYR B 586 ARG 0.010 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 42) link_NAG-ASN : angle 2.93904 ( 126) link_ALPHA1-6 : bond 0.01380 ( 6) link_ALPHA1-6 : angle 3.39305 ( 18) link_BETA1-4 : bond 0.00482 ( 30) link_BETA1-4 : angle 2.37103 ( 90) link_ALPHA1-3 : bond 0.00904 ( 9) link_ALPHA1-3 : angle 2.61497 ( 27) hydrogen bonds : bond 0.04132 ( 345) hydrogen bonds : angle 6.50664 ( 927) SS BOND : bond 0.00496 ( 27) SS BOND : angle 1.11875 ( 54) covalent geometry : bond 0.00494 (15969) covalent geometry : angle 0.79205 (21732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9539 (tptp) cc_final: 0.9204 (tptp) REVERT: B 588 LYS cc_start: 0.9789 (tmtt) cc_final: 0.9571 (tptp) REVERT: B 652 GLN cc_start: 0.9708 (tt0) cc_final: 0.9467 (tm-30) REVERT: G 250 MET cc_start: 0.9147 (mmp) cc_final: 0.8856 (tpp) REVERT: G 468 MET cc_start: 0.6833 (tmm) cc_final: 0.6207 (ppp) REVERT: H 60 TYR cc_start: 0.8928 (m-80) cc_final: 0.8696 (m-10) REVERT: L 30 ASP cc_start: 0.9344 (t0) cc_final: 0.9137 (t0) REVERT: A 639 GLU cc_start: 0.9142 (pp20) cc_final: 0.8909 (pp20) REVERT: A 652 GLN cc_start: 0.9693 (tt0) cc_final: 0.9470 (tm-30) REVERT: C 250 MET cc_start: 0.9164 (mmp) cc_final: 0.8849 (tpp) REVERT: C 374 MET cc_start: 0.7826 (pmm) cc_final: 0.7449 (pmm) REVERT: C 468 MET cc_start: 0.6265 (tmm) cc_final: 0.5602 (ppp) REVERT: D 66 LYS cc_start: 0.7303 (pttm) cc_final: 0.7018 (pptt) REVERT: F 574 LYS cc_start: 0.9489 (tptp) cc_final: 0.9193 (tptp) REVERT: F 588 LYS cc_start: 0.9720 (tmtt) cc_final: 0.9511 (tptp) REVERT: F 639 GLU cc_start: 0.9265 (pp20) cc_final: 0.9027 (pp20) REVERT: I 468 MET cc_start: 0.4606 (tmm) cc_final: 0.3914 (ppp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2784 time to fit residues: 45.9000 Evaluate side-chains 91 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 32 optimal weight: 0.6980 chunk 169 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.042749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.033439 restraints weight = 173421.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.034294 restraints weight = 120003.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.034852 restraints weight = 94803.860| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16083 Z= 0.124 Angle : 0.749 11.749 22047 Z= 0.341 Chirality : 0.050 0.381 2643 Planarity : 0.004 0.047 2619 Dihedral : 9.040 106.311 3738 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.19), residues: 1773 helix: 0.10 (0.28), residues: 291 sheet: -0.77 (0.26), residues: 405 loop : -1.79 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 338 HIS 0.001 0.000 HIS G 352 PHE 0.015 0.001 PHE A 637 TYR 0.036 0.001 TYR K 92 ARG 0.005 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 42) link_NAG-ASN : angle 2.97353 ( 126) link_ALPHA1-6 : bond 0.01517 ( 6) link_ALPHA1-6 : angle 3.13009 ( 18) link_BETA1-4 : bond 0.00377 ( 30) link_BETA1-4 : angle 2.18576 ( 90) link_ALPHA1-3 : bond 0.00763 ( 9) link_ALPHA1-3 : angle 2.65816 ( 27) hydrogen bonds : bond 0.03496 ( 345) hydrogen bonds : angle 6.05503 ( 927) SS BOND : bond 0.00578 ( 27) SS BOND : angle 1.04175 ( 54) covalent geometry : bond 0.00256 (15969) covalent geometry : angle 0.69186 (21732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9592 (tptp) cc_final: 0.9217 (tptp) REVERT: B 588 LYS cc_start: 0.9819 (tmtt) cc_final: 0.9596 (tptp) REVERT: B 639 GLU cc_start: 0.9292 (pp20) cc_final: 0.9035 (pp20) REVERT: B 652 GLN cc_start: 0.9739 (tt0) cc_final: 0.9467 (tm-30) REVERT: G 250 MET cc_start: 0.9273 (mmp) cc_final: 0.8843 (tpp) REVERT: G 468 MET cc_start: 0.6729 (tmm) cc_final: 0.5784 (ppp) REVERT: H 60 TYR cc_start: 0.9053 (m-80) cc_final: 0.8806 (m-10) REVERT: L 30 ASP cc_start: 0.9431 (t0) cc_final: 0.9190 (t0) REVERT: A 584 GLU cc_start: 0.9279 (pp20) cc_final: 0.9057 (pp20) REVERT: A 639 GLU cc_start: 0.9165 (pp20) cc_final: 0.8899 (pp20) REVERT: A 652 GLN cc_start: 0.9718 (tt0) cc_final: 0.9402 (tm-30) REVERT: C 250 MET cc_start: 0.9379 (mmp) cc_final: 0.8749 (tpp) REVERT: C 468 MET cc_start: 0.6918 (tmm) cc_final: 0.6375 (ppp) REVERT: E 4 MET cc_start: 0.8093 (mmp) cc_final: 0.7799 (mmm) REVERT: F 574 LYS cc_start: 0.9558 (tptp) cc_final: 0.9264 (tptp) REVERT: F 588 LYS cc_start: 0.9763 (tmtt) cc_final: 0.9506 (tptp) REVERT: F 639 GLU cc_start: 0.9272 (pp20) cc_final: 0.8958 (pp20) REVERT: I 468 MET cc_start: 0.4238 (tmm) cc_final: 0.3933 (ppp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2748 time to fit residues: 50.7026 Evaluate side-chains 92 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 152 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 42 optimal weight: 0.0670 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.041920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.032764 restraints weight = 175688.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.033603 restraints weight = 121237.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.034173 restraints weight = 95572.469| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.7287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16083 Z= 0.144 Angle : 0.734 9.719 22047 Z= 0.335 Chirality : 0.048 0.363 2643 Planarity : 0.004 0.041 2619 Dihedral : 8.758 103.646 3738 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.65 (0.20), residues: 1773 helix: 0.25 (0.28), residues: 291 sheet: -0.60 (0.26), residues: 402 loop : -1.75 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 610 HIS 0.001 0.001 HIS G 275 PHE 0.017 0.001 PHE B 600 TYR 0.018 0.001 TYR B 586 ARG 0.007 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 42) link_NAG-ASN : angle 2.87025 ( 126) link_ALPHA1-6 : bond 0.01338 ( 6) link_ALPHA1-6 : angle 2.99357 ( 18) link_BETA1-4 : bond 0.00389 ( 30) link_BETA1-4 : angle 2.14854 ( 90) link_ALPHA1-3 : bond 0.00721 ( 9) link_ALPHA1-3 : angle 2.48508 ( 27) hydrogen bonds : bond 0.03415 ( 345) hydrogen bonds : angle 6.01278 ( 927) SS BOND : bond 0.00313 ( 27) SS BOND : angle 0.94189 ( 54) covalent geometry : bond 0.00307 (15969) covalent geometry : angle 0.68018 (21732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9601 (tptp) cc_final: 0.9247 (tptp) REVERT: B 588 LYS cc_start: 0.9807 (tmtt) cc_final: 0.9546 (tptp) REVERT: B 639 GLU cc_start: 0.9274 (pp20) cc_final: 0.9029 (pp20) REVERT: G 250 MET cc_start: 0.9255 (mmp) cc_final: 0.8846 (tpp) REVERT: H 60 TYR cc_start: 0.9005 (m-80) cc_final: 0.8723 (m-10) REVERT: L 30 ASP cc_start: 0.9417 (t0) cc_final: 0.9204 (t0) REVERT: A 639 GLU cc_start: 0.9142 (pp20) cc_final: 0.8901 (pp20) REVERT: A 652 GLN cc_start: 0.9713 (tt0) cc_final: 0.9470 (tm-30) REVERT: C 250 MET cc_start: 0.9342 (mmp) cc_final: 0.8696 (tpp) REVERT: C 468 MET cc_start: 0.6423 (tmm) cc_final: 0.5739 (ppp) REVERT: D 60 TYR cc_start: 0.9025 (m-80) cc_final: 0.8697 (m-80) REVERT: E 4 MET cc_start: 0.8164 (mmp) cc_final: 0.7882 (mmm) REVERT: F 574 LYS cc_start: 0.9563 (tptp) cc_final: 0.9301 (tptp) REVERT: F 588 LYS cc_start: 0.9752 (tmtt) cc_final: 0.9513 (tptp) REVERT: F 639 GLU cc_start: 0.9279 (pp20) cc_final: 0.8990 (pp20) REVERT: I 468 MET cc_start: 0.4638 (tmm) cc_final: 0.4324 (ppp) REVERT: J 3 GLN cc_start: 0.8573 (pm20) cc_final: 0.8091 (mm-40) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2816 time to fit residues: 50.5038 Evaluate side-chains 92 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 23 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.042388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033160 restraints weight = 175089.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.034006 restraints weight = 120054.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.034585 restraints weight = 94349.750| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16083 Z= 0.117 Angle : 0.726 12.330 22047 Z= 0.329 Chirality : 0.049 0.373 2643 Planarity : 0.004 0.040 2619 Dihedral : 8.588 101.761 3738 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.20), residues: 1773 helix: 0.26 (0.28), residues: 288 sheet: -0.55 (0.26), residues: 408 loop : -1.68 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 338 HIS 0.003 0.001 HIS K 55 PHE 0.014 0.001 PHE A 637 TYR 0.010 0.001 TYR L 32 ARG 0.004 0.000 ARG K 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 42) link_NAG-ASN : angle 2.80332 ( 126) link_ALPHA1-6 : bond 0.01342 ( 6) link_ALPHA1-6 : angle 2.81812 ( 18) link_BETA1-4 : bond 0.00407 ( 30) link_BETA1-4 : angle 2.12457 ( 90) link_ALPHA1-3 : bond 0.00680 ( 9) link_ALPHA1-3 : angle 2.49419 ( 27) hydrogen bonds : bond 0.03259 ( 345) hydrogen bonds : angle 5.84195 ( 927) SS BOND : bond 0.00293 ( 27) SS BOND : angle 0.79948 ( 54) covalent geometry : bond 0.00250 (15969) covalent geometry : angle 0.67407 (21732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9602 (tptp) cc_final: 0.9254 (tptp) REVERT: B 588 LYS cc_start: 0.9813 (tmtt) cc_final: 0.9544 (tptp) REVERT: B 639 GLU cc_start: 0.9298 (pp20) cc_final: 0.9016 (pp20) REVERT: G 250 MET cc_start: 0.9313 (mmp) cc_final: 0.8775 (tpp) REVERT: L 30 ASP cc_start: 0.9417 (t0) cc_final: 0.9189 (t0) REVERT: A 639 GLU cc_start: 0.9128 (pp20) cc_final: 0.8868 (pp20) REVERT: A 652 GLN cc_start: 0.9730 (tt0) cc_final: 0.9467 (tm-30) REVERT: C 250 MET cc_start: 0.9376 (mmp) cc_final: 0.8628 (tpp) REVERT: C 468 MET cc_start: 0.6714 (tmm) cc_final: 0.6066 (ppp) REVERT: D 60 TYR cc_start: 0.9083 (m-80) cc_final: 0.8764 (m-80) REVERT: E 4 MET cc_start: 0.8105 (mmp) cc_final: 0.7849 (mmm) REVERT: F 588 LYS cc_start: 0.9763 (tmtt) cc_final: 0.9510 (tptp) REVERT: F 639 GLU cc_start: 0.9294 (pp20) cc_final: 0.9006 (pp20) REVERT: I 468 MET cc_start: 0.4826 (tmm) cc_final: 0.4489 (ppp) REVERT: J 3 GLN cc_start: 0.8599 (pm20) cc_final: 0.8021 (mm-40) REVERT: K 4 MET cc_start: 0.8434 (mmp) cc_final: 0.8199 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2803 time to fit residues: 50.2345 Evaluate side-chains 94 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 111 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 157 optimal weight: 0.0070 chunk 106 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.040855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.031946 restraints weight = 178700.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.032716 restraints weight = 124293.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.033273 restraints weight = 98822.754| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16083 Z= 0.184 Angle : 0.752 9.595 22047 Z= 0.348 Chirality : 0.048 0.362 2643 Planarity : 0.004 0.046 2619 Dihedral : 8.568 98.267 3738 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.62 (0.20), residues: 1773 helix: 0.28 (0.28), residues: 291 sheet: -0.74 (0.26), residues: 411 loop : -1.66 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 610 HIS 0.002 0.001 HIS L 55 PHE 0.017 0.002 PHE A 637 TYR 0.026 0.002 TYR K 92 ARG 0.006 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 42) link_NAG-ASN : angle 2.80135 ( 126) link_ALPHA1-6 : bond 0.01119 ( 6) link_ALPHA1-6 : angle 2.79004 ( 18) link_BETA1-4 : bond 0.00386 ( 30) link_BETA1-4 : angle 2.18530 ( 90) link_ALPHA1-3 : bond 0.00640 ( 9) link_ALPHA1-3 : angle 2.40288 ( 27) hydrogen bonds : bond 0.03555 ( 345) hydrogen bonds : angle 6.06377 ( 927) SS BOND : bond 0.00339 ( 27) SS BOND : angle 0.86389 ( 54) covalent geometry : bond 0.00390 (15969) covalent geometry : angle 0.70200 (21732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4104.53 seconds wall clock time: 73 minutes 37.24 seconds (4417.24 seconds total)