Starting phenix.real_space_refine on Sat Jun 14 03:06:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dua_27718/06_2025/8dua_27718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dua_27718/06_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_27718/06_2025/8dua_27718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dua_27718/06_2025/8dua_27718.map" model { file = "/net/cci-nas-00/data/ceres_data/8dua_27718/06_2025/8dua_27718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dua_27718/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.15, per 1000 atoms: 0.65 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: 5.27 Conformation dependent library (CDL) restraints added in 1.9 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: 2.13 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: 4.44 Time building geometry restraints manager: 6.04 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: 0.03 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: 2.170 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 39.200 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.160 ------------------------------------------------------------------------------- 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 : 1.925 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: 0.3676 time to fit residues: 130.5017 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 : 2.166 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.041436 restraints weight = 169219.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.042268 restraints weight = 123430.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.042876 restraints weight = 100180.945| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 2.578 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: 0.9083 (tp-100) REVERT: B 639 GLU cc_start: 0.9172 (pp20) cc_final: 0.8918 (pp20) REVERT: B 652 GLN cc_start: 0.9703 (tt0) cc_final: 0.9369 (tm-30) REVERT: G 250 MET cc_start: 0.9161 (mmp) cc_final: 0.8420 (tpp) REVERT: G 468 MET cc_start: 0.3157 (ttp) cc_final: 0.2290 (pmm) REVERT: H 72 ASP cc_start: 0.8602 (p0) cc_final: 0.8288 (p0) REVERT: A 652 GLN cc_start: 0.9705 (tt0) cc_final: 0.9303 (tm-30) REVERT: C 468 MET cc_start: 0.3813 (tmm) cc_final: 0.3498 (tmm) REVERT: D 58 THR cc_start: 0.8723 (p) cc_final: 0.8283 (t) REVERT: D 60 TYR cc_start: 0.8803 (m-10) cc_final: 0.8379 (m-80) REVERT: F 639 GLU cc_start: 0.8990 (pp20) cc_final: 0.8763 (pp20) REVERT: I 479 TYR cc_start: 0.8547 (m-80) cc_final: 0.8271 (m-80) REVERT: J 86 ASP cc_start: 0.7965 (m-30) cc_final: 0.7646 (m-30) REVERT: J 90 TYR cc_start: 0.8831 (m-80) cc_final: 0.8372 (m-80) REVERT: J 107 LEU cc_start: 0.9210 (tp) cc_final: 0.8996 (tp) REVERT: K 30 ASP cc_start: 0.9393 (t70) cc_final: 0.8777 (t0) outliers start: 6 outliers final: 0 residues processed: 169 average time/residue: 0.3399 time to fit residues: 84.4349 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 : 1.731 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 135 optimal weight: 0.0050 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.050390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.040555 restraints weight = 167423.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.041421 restraints weight = 122207.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.042009 restraints weight = 98709.607| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16083 Z= 0.138 Angle : 0.731 10.354 22047 Z= 0.332 Chirality : 0.050 0.341 2643 Planarity : 0.004 0.058 2619 Dihedral : 12.890 114.112 3738 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.25 % Allowed : 2.39 % Favored : 97.36 % 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: -1.52 (0.19), residues: 1773 helix: -0.29 (0.30), residues: 273 sheet: 0.41 (0.30), residues: 261 loop : -1.60 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 610 HIS 0.001 0.000 HIS I 275 PHE 0.018 0.001 PHE B 600 TYR 0.016 0.001 TYR B 586 ARG 0.009 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 42) link_NAG-ASN : angle 2.94662 ( 126) link_ALPHA1-6 : bond 0.01499 ( 6) link_ALPHA1-6 : angle 3.31893 ( 18) link_BETA1-4 : bond 0.00520 ( 30) link_BETA1-4 : angle 2.34011 ( 90) link_ALPHA1-3 : bond 0.01070 ( 9) link_ALPHA1-3 : angle 2.77979 ( 27) hydrogen bonds : bond 0.04876 ( 345) hydrogen bonds : angle 6.51413 ( 927) SS BOND : bond 0.00296 ( 27) SS BOND : angle 0.59530 ( 54) covalent geometry : bond 0.00286 (15969) covalent geometry : angle 0.67078 (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 154 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 583 ILE cc_start: 0.9751 (OUTLIER) cc_final: 0.9421 (tp) REVERT: B 584 GLU cc_start: 0.9436 (OUTLIER) cc_final: 0.9107 (pp20) REVERT: B 588 LYS cc_start: 0.9708 (tmtt) cc_final: 0.9501 (tptp) REVERT: B 652 GLN cc_start: 0.9679 (tt0) cc_final: 0.9397 (tm-30) REVERT: G 250 MET cc_start: 0.9184 (mmp) cc_final: 0.8498 (tpp) REVERT: G 468 MET cc_start: 0.4172 (tmm) cc_final: 0.3443 (tmm) REVERT: H 60 TYR cc_start: 0.8808 (m-80) cc_final: 0.8600 (m-80) REVERT: H 72 ASP cc_start: 0.8524 (p0) cc_final: 0.8270 (p0) REVERT: A 652 GLN cc_start: 0.9647 (tt0) cc_final: 0.9287 (tm-30) REVERT: C 250 MET cc_start: 0.9251 (mmm) cc_final: 0.8653 (tpp) REVERT: C 468 MET cc_start: 0.3678 (tmm) cc_final: 0.3248 (tmm) REVERT: D 58 THR cc_start: 0.8775 (p) cc_final: 0.7549 (p) REVERT: D 60 TYR cc_start: 0.8888 (m-10) cc_final: 0.8673 (m-10) REVERT: F 639 GLU cc_start: 0.9023 (pp20) cc_final: 0.8695 (pp20) REVERT: J 86 ASP cc_start: 0.7957 (m-30) cc_final: 0.7579 (m-30) REVERT: J 90 TYR cc_start: 0.8765 (m-80) cc_final: 0.8313 (m-10) REVERT: J 107 LEU cc_start: 0.9206 (tp) cc_final: 0.8994 (tp) REVERT: K 3 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7625 (mm-40) REVERT: K 30 ASP cc_start: 0.9367 (t70) cc_final: 0.8742 (t0) outliers start: 4 outliers final: 0 residues processed: 150 average time/residue: 0.3205 time to fit residues: 72.2733 Evaluate side-chains 119 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 134 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN C 73 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.046809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.037289 restraints weight = 170791.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038142 restraints weight = 121304.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.038728 restraints weight = 96834.692| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 16083 Z= 0.193 Angle : 0.780 9.877 22047 Z= 0.360 Chirality : 0.050 0.343 2643 Planarity : 0.005 0.057 2619 Dihedral : 10.679 112.266 3738 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.25 % Allowed : 4.77 % Favored : 94.98 % 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: -1.69 (0.18), residues: 1773 helix: -0.28 (0.28), residues: 297 sheet: 0.28 (0.30), residues: 246 loop : -1.75 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 610 HIS 0.002 0.001 HIS L 55 PHE 0.015 0.002 PHE C 53 TYR 0.023 0.002 TYR B 586 ARG 0.014 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 42) link_NAG-ASN : angle 2.87164 ( 126) link_ALPHA1-6 : bond 0.01483 ( 6) link_ALPHA1-6 : angle 2.35712 ( 18) link_BETA1-4 : bond 0.00461 ( 30) link_BETA1-4 : angle 2.04354 ( 90) link_ALPHA1-3 : bond 0.01046 ( 9) link_ALPHA1-3 : angle 3.07701 ( 27) hydrogen bonds : bond 0.03958 ( 345) hydrogen bonds : angle 6.29358 ( 927) SS BOND : bond 0.00315 ( 27) SS BOND : angle 0.97138 ( 54) covalent geometry : bond 0.00412 (15969) covalent geometry : angle 0.73065 (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 143 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9530 (tptp) cc_final: 0.9170 (tptp) REVERT: B 583 ILE cc_start: 0.9758 (OUTLIER) cc_final: 0.9504 (tp) REVERT: B 588 LYS cc_start: 0.9765 (tmtt) cc_final: 0.9540 (tptp) REVERT: B 639 GLU cc_start: 0.9200 (pp20) cc_final: 0.8949 (pp20) REVERT: B 652 GLN cc_start: 0.9706 (tt0) cc_final: 0.9422 (tm-30) REVERT: G 250 MET cc_start: 0.9342 (mmp) cc_final: 0.8728 (tpp) REVERT: G 468 MET cc_start: 0.5034 (tmm) cc_final: 0.4172 (ppp) REVERT: H 60 TYR cc_start: 0.8986 (m-80) cc_final: 0.8782 (m-10) REVERT: A 587 LEU cc_start: 0.9417 (pp) cc_final: 0.9075 (pp) REVERT: A 652 GLN cc_start: 0.9680 (tt0) cc_final: 0.9275 (tm-30) REVERT: C 250 MET cc_start: 0.9231 (mmm) cc_final: 0.9026 (tpp) REVERT: C 468 MET cc_start: 0.4762 (tmm) cc_final: 0.3946 (tmm) REVERT: D 58 THR cc_start: 0.8644 (p) cc_final: 0.7396 (p) REVERT: F 583 ILE cc_start: 0.9726 (OUTLIER) cc_final: 0.9356 (tp) REVERT: F 639 GLU cc_start: 0.9186 (pp20) cc_final: 0.8882 (pp20) REVERT: J 107 LEU cc_start: 0.9291 (tp) cc_final: 0.9048 (tp) REVERT: K 30 ASP cc_start: 0.9381 (t70) cc_final: 0.8802 (t0) outliers start: 4 outliers final: 0 residues processed: 139 average time/residue: 0.3406 time to fit residues: 71.1409 Evaluate side-chains 110 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 2.722 ------------------------------------------------------------------------------- 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: 6.9990 chunk 155 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 36 optimal weight: 0.1980 chunk 29 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** J 39 GLN ** 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 = 0.3438 r_free = 0.3438 target = 0.047030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.037410 restraints weight = 172572.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.038210 restraints weight = 124421.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.038794 restraints weight = 100770.767| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16083 Z= 0.130 Angle : 0.724 10.049 22047 Z= 0.326 Chirality : 0.050 0.340 2643 Planarity : 0.004 0.029 2619 Dihedral : 9.978 111.743 3738 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.13 % Allowed : 1.63 % Favored : 98.24 % 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: -1.52 (0.19), residues: 1773 helix: -0.14 (0.29), residues: 273 sheet: 0.28 (0.28), residues: 288 loop : -1.65 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 610 HIS 0.002 0.000 HIS G 352 PHE 0.010 0.001 PHE B 600 TYR 0.020 0.001 TYR F 586 ARG 0.005 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 42) link_NAG-ASN : angle 2.77039 ( 126) link_ALPHA1-6 : bond 0.01725 ( 6) link_ALPHA1-6 : angle 2.73800 ( 18) link_BETA1-4 : bond 0.00393 ( 30) link_BETA1-4 : angle 2.06004 ( 90) link_ALPHA1-3 : bond 0.00977 ( 9) link_ALPHA1-3 : angle 2.86753 ( 27) hydrogen bonds : bond 0.03820 ( 345) hydrogen bonds : angle 5.89961 ( 927) SS BOND : bond 0.00245 ( 27) SS BOND : angle 0.62853 ( 54) covalent geometry : bond 0.00268 (15969) covalent geometry : angle 0.67231 (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 142 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9550 (tptp) cc_final: 0.9212 (tptp) REVERT: B 583 ILE cc_start: 0.9788 (OUTLIER) cc_final: 0.9376 (tp) REVERT: B 588 LYS cc_start: 0.9776 (tmtt) cc_final: 0.9519 (tptp) REVERT: B 639 GLU cc_start: 0.9205 (pp20) cc_final: 0.8950 (pp20) REVERT: B 652 GLN cc_start: 0.9713 (tt0) cc_final: 0.9432 (tm-30) REVERT: G 250 MET cc_start: 0.9341 (mmp) cc_final: 0.8752 (tpp) REVERT: G 468 MET cc_start: 0.5507 (tmm) cc_final: 0.4731 (ppp) REVERT: H 60 TYR cc_start: 0.8955 (m-80) cc_final: 0.8712 (m-10) REVERT: A 639 GLU cc_start: 0.9275 (pp20) cc_final: 0.8924 (pp20) REVERT: C 468 MET cc_start: 0.5149 (tmm) cc_final: 0.4531 (ppp) REVERT: D 58 THR cc_start: 0.8139 (p) cc_final: 0.6796 (p) REVERT: D 60 TYR cc_start: 0.8708 (m-80) cc_final: 0.8105 (m-10) REVERT: E 70 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8860 (mmmt) REVERT: F 588 LYS cc_start: 0.9720 (tmtt) cc_final: 0.9502 (tptp) REVERT: F 639 GLU cc_start: 0.9180 (pp20) cc_final: 0.8831 (pp20) REVERT: I 468 MET cc_start: 0.1883 (tmm) cc_final: 0.1544 (tmm) REVERT: J 107 LEU cc_start: 0.9259 (tp) cc_final: 0.9021 (tp) REVERT: K 30 ASP cc_start: 0.9353 (t70) cc_final: 0.8802 (t0) outliers start: 2 outliers final: 1 residues processed: 140 average time/residue: 0.2736 time to fit residues: 57.5554 Evaluate side-chains 110 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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: 10.0000 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.043875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.034595 restraints weight = 175683.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.035349 restraints weight = 126085.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.035888 restraints weight = 102145.990| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16083 Z= 0.194 Angle : 0.782 9.624 22047 Z= 0.361 Chirality : 0.049 0.335 2643 Planarity : 0.004 0.044 2619 Dihedral : 9.252 109.704 3738 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.06 % Allowed : 2.95 % 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: -1.68 (0.19), residues: 1773 helix: -0.02 (0.28), residues: 291 sheet: -0.41 (0.26), residues: 354 loop : -1.74 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 610 HIS 0.003 0.001 HIS L 55 PHE 0.017 0.002 PHE L 62 TYR 0.024 0.002 TYR B 586 ARG 0.013 0.001 ARG C 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 42) link_NAG-ASN : angle 2.85117 ( 126) link_ALPHA1-6 : bond 0.01555 ( 6) link_ALPHA1-6 : angle 3.57549 ( 18) link_BETA1-4 : bond 0.00471 ( 30) link_BETA1-4 : angle 2.09892 ( 90) link_ALPHA1-3 : bond 0.00973 ( 9) link_ALPHA1-3 : angle 2.73980 ( 27) hydrogen bonds : bond 0.03865 ( 345) hydrogen bonds : angle 6.10803 ( 927) SS BOND : bond 0.01021 ( 27) SS BOND : angle 1.02291 ( 54) covalent geometry : bond 0.00401 (15969) covalent geometry : angle 0.72927 (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 128 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9589 (tptp) cc_final: 0.9218 (tptp) REVERT: B 588 LYS cc_start: 0.9817 (tmtt) cc_final: 0.9571 (tptp) REVERT: B 639 GLU cc_start: 0.9304 (pp20) cc_final: 0.9077 (pp20) REVERT: B 652 GLN cc_start: 0.9713 (tt0) cc_final: 0.9428 (tm-30) REVERT: G 250 MET cc_start: 0.9277 (mmp) cc_final: 0.8817 (tpp) REVERT: G 468 MET cc_start: 0.6182 (tmm) cc_final: 0.5396 (ppp) REVERT: H 60 TYR cc_start: 0.9039 (m-80) cc_final: 0.8736 (m-10) REVERT: A 639 GLU cc_start: 0.9331 (pp20) cc_final: 0.8927 (pp20) REVERT: A 652 GLN cc_start: 0.9704 (tt0) cc_final: 0.9336 (tm-30) REVERT: C 250 MET cc_start: 0.9220 (mmp) cc_final: 0.8809 (mmp) REVERT: C 468 MET cc_start: 0.5392 (tmm) cc_final: 0.4633 (ppp) REVERT: D 3 GLN cc_start: 0.8453 (mp-120) cc_final: 0.8208 (pm20) REVERT: D 58 THR cc_start: 0.8359 (p) cc_final: 0.7252 (p) REVERT: D 60 TYR cc_start: 0.8701 (m-80) cc_final: 0.8073 (m-10) REVERT: E 4 MET cc_start: 0.7467 (mmp) cc_final: 0.7116 (mmm) REVERT: F 574 LYS cc_start: 0.9539 (tptp) cc_final: 0.9235 (tptp) REVERT: F 639 GLU cc_start: 0.9259 (pp20) cc_final: 0.8955 (pp20) REVERT: I 468 MET cc_start: 0.2748 (tmm) cc_final: 0.2369 (tmm) REVERT: J 107 LEU cc_start: 0.9310 (tp) cc_final: 0.9094 (tp) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2635 time to fit residues: 51.0948 Evaluate side-chains 98 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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: 4.9990 chunk 170 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN H 39 GLN ** 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** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.042149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033047 restraints weight = 186720.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.033845 restraints weight = 132126.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.034390 restraints weight = 105949.740| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16083 Z= 0.198 Angle : 0.783 9.472 22047 Z= 0.359 Chirality : 0.052 0.418 2643 Planarity : 0.004 0.047 2619 Dihedral : 9.251 107.038 3738 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 (0.27), residues: 291 sheet: -0.74 (0.26), residues: 363 loop : -1.79 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 36 HIS 0.003 0.001 HIS C 275 PHE 0.014 0.002 PHE K 71 TYR 0.026 0.002 TYR B 586 ARG 0.014 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 42) link_NAG-ASN : angle 2.77748 ( 126) link_ALPHA1-6 : bond 0.01647 ( 6) link_ALPHA1-6 : angle 2.93236 ( 18) link_BETA1-4 : bond 0.00375 ( 30) link_BETA1-4 : angle 2.24604 ( 90) link_ALPHA1-3 : bond 0.00743 ( 9) link_ALPHA1-3 : angle 2.69146 ( 27) hydrogen bonds : bond 0.03754 ( 345) hydrogen bonds : angle 6.19719 ( 927) SS BOND : bond 0.00514 ( 27) SS BOND : angle 0.95989 ( 54) covalent geometry : bond 0.00413 (15969) covalent geometry : angle 0.73324 (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 119 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9554 (tptp) cc_final: 0.9170 (tptp) REVERT: B 639 GLU cc_start: 0.9203 (pp20) cc_final: 0.8995 (pp20) REVERT: B 652 GLN cc_start: 0.9646 (tt0) cc_final: 0.9418 (tm-30) REVERT: G 250 MET cc_start: 0.9173 (mmp) cc_final: 0.8810 (tpp) REVERT: G 468 MET cc_start: 0.6537 (tmm) cc_final: 0.5831 (ppp) REVERT: H 60 TYR cc_start: 0.9025 (m-80) cc_final: 0.8763 (m-10) REVERT: A 639 GLU cc_start: 0.9285 (pp20) cc_final: 0.8971 (pp20) REVERT: A 652 GLN cc_start: 0.9623 (tt0) cc_final: 0.9312 (tm-30) REVERT: C 250 MET cc_start: 0.9205 (mmp) cc_final: 0.8648 (tpp) REVERT: C 468 MET cc_start: 0.6003 (tmm) cc_final: 0.5306 (ppp) REVERT: D 58 THR cc_start: 0.8117 (p) cc_final: 0.6976 (p) REVERT: D 60 TYR cc_start: 0.8662 (m-80) cc_final: 0.8029 (m-10) REVERT: F 574 LYS cc_start: 0.9474 (tptp) cc_final: 0.9111 (tptt) REVERT: F 588 LYS cc_start: 0.9744 (tmtt) cc_final: 0.9521 (tptp) REVERT: F 639 GLU cc_start: 0.9203 (pp20) cc_final: 0.8932 (pp20) REVERT: I 374 MET cc_start: 0.5922 (pmm) cc_final: 0.5500 (pmm) REVERT: I 468 MET cc_start: 0.4071 (tmm) cc_final: 0.3423 (tmm) REVERT: J 107 LEU cc_start: 0.9283 (tp) cc_final: 0.9070 (tp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2800 time to fit residues: 50.7340 Evaluate side-chains 90 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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: 4.9990 chunk 169 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.042174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.033064 restraints weight = 177750.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.033859 restraints weight = 124810.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.034414 restraints weight = 99446.727| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16083 Z= 0.164 Angle : 0.749 10.068 22047 Z= 0.342 Chirality : 0.049 0.336 2643 Planarity : 0.004 0.041 2619 Dihedral : 8.897 104.632 3738 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -1.75 (0.19), residues: 1773 helix: 0.20 (0.28), residues: 291 sheet: -0.74 (0.26), residues: 390 loop : -1.79 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 332 HIS 0.002 0.001 HIS L 55 PHE 0.015 0.002 PHE B 600 TYR 0.021 0.001 TYR B 586 ARG 0.006 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 42) link_NAG-ASN : angle 2.91501 ( 126) link_ALPHA1-6 : bond 0.01349 ( 6) link_ALPHA1-6 : angle 3.20789 ( 18) link_BETA1-4 : bond 0.00389 ( 30) link_BETA1-4 : angle 2.13554 ( 90) link_ALPHA1-3 : bond 0.00765 ( 9) link_ALPHA1-3 : angle 2.55498 ( 27) hydrogen bonds : bond 0.03603 ( 345) hydrogen bonds : angle 6.09610 ( 927) SS BOND : bond 0.00523 ( 27) SS BOND : angle 0.90044 ( 54) covalent geometry : bond 0.00343 (15969) covalent geometry : angle 0.69441 (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 119 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9574 (tptp) cc_final: 0.9177 (tptp) REVERT: B 588 LYS cc_start: 0.9785 (tmtt) cc_final: 0.9518 (tptp) REVERT: B 639 GLU cc_start: 0.9268 (pp20) cc_final: 0.9032 (pp20) REVERT: B 652 GLN cc_start: 0.9729 (tt0) cc_final: 0.9480 (tm-30) REVERT: G 250 MET cc_start: 0.9249 (mmp) cc_final: 0.8876 (tpp) REVERT: H 60 TYR cc_start: 0.8928 (m-80) cc_final: 0.8652 (m-10) REVERT: A 639 GLU cc_start: 0.9357 (pp20) cc_final: 0.8998 (pp20) REVERT: A 652 GLN cc_start: 0.9685 (tt0) cc_final: 0.9352 (tm-30) REVERT: C 250 MET cc_start: 0.9308 (mmp) cc_final: 0.8613 (tpp) REVERT: C 468 MET cc_start: 0.6298 (tmm) cc_final: 0.5607 (ppp) REVERT: D 58 THR cc_start: 0.8120 (p) cc_final: 0.7352 (p) REVERT: D 60 TYR cc_start: 0.8636 (m-80) cc_final: 0.7985 (m-10) REVERT: E 4 MET cc_start: 0.7987 (mmp) cc_final: 0.7772 (mmm) REVERT: F 574 LYS cc_start: 0.9544 (tptp) cc_final: 0.9280 (tptp) REVERT: F 588 LYS cc_start: 0.9766 (tmtt) cc_final: 0.9527 (tptp) REVERT: F 639 GLU cc_start: 0.9283 (pp20) cc_final: 0.8986 (pp20) REVERT: I 374 MET cc_start: 0.6220 (pmm) cc_final: 0.5653 (pmm) REVERT: I 468 MET cc_start: 0.4566 (tmm) cc_final: 0.3837 (tmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3276 time to fit residues: 59.9345 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 : 2.353 ------------------------------------------------------------------------------- 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: 9.9990 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** D 39 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.041804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.032736 restraints weight = 176776.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.033549 restraints weight = 123206.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.034087 restraints weight = 97879.570| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16083 Z= 0.148 Angle : 0.735 9.494 22047 Z= 0.334 Chirality : 0.049 0.340 2643 Planarity : 0.004 0.043 2619 Dihedral : 8.751 102.056 3738 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.66 (0.19), residues: 1773 helix: 0.25 (0.28), residues: 291 sheet: -0.66 (0.26), residues: 405 loop : -1.74 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 338 HIS 0.001 0.000 HIS C 275 PHE 0.014 0.001 PHE B 600 TYR 0.017 0.001 TYR B 586 ARG 0.005 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 42) link_NAG-ASN : angle 2.76887 ( 126) link_ALPHA1-6 : bond 0.01317 ( 6) link_ALPHA1-6 : angle 2.84023 ( 18) link_BETA1-4 : bond 0.00370 ( 30) link_BETA1-4 : angle 2.15115 ( 90) link_ALPHA1-3 : bond 0.00674 ( 9) link_ALPHA1-3 : angle 2.51086 ( 27) hydrogen bonds : bond 0.03436 ( 345) hydrogen bonds : angle 6.02815 ( 927) SS BOND : bond 0.00350 ( 27) SS BOND : angle 0.84549 ( 54) covalent geometry : bond 0.00314 (15969) covalent geometry : angle 0.68407 (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 116 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 5.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9600 (tptp) cc_final: 0.9257 (tptp) REVERT: B 588 LYS cc_start: 0.9790 (tmtt) cc_final: 0.9510 (tptp) REVERT: B 639 GLU cc_start: 0.9283 (pp20) cc_final: 0.9029 (pp20) REVERT: G 250 MET cc_start: 0.9271 (mmp) cc_final: 0.8838 (tpp) REVERT: H 60 TYR cc_start: 0.8953 (m-80) cc_final: 0.8645 (m-10) REVERT: A 639 GLU cc_start: 0.9364 (pp20) cc_final: 0.9026 (pp20) REVERT: A 652 GLN cc_start: 0.9712 (tt0) cc_final: 0.9409 (tm-30) REVERT: C 250 MET cc_start: 0.9342 (mmp) cc_final: 0.8688 (tpp) REVERT: C 468 MET cc_start: 0.6413 (tmm) cc_final: 0.5721 (ppp) REVERT: D 58 THR cc_start: 0.8041 (p) cc_final: 0.7303 (p) REVERT: D 60 TYR cc_start: 0.8671 (m-80) cc_final: 0.7994 (m-10) REVERT: F 574 LYS cc_start: 0.9561 (tptp) cc_final: 0.9282 (tptp) REVERT: F 588 LYS cc_start: 0.9769 (tmtt) cc_final: 0.9549 (tptp) REVERT: F 639 GLU cc_start: 0.9273 (pp20) cc_final: 0.9010 (pp20) REVERT: I 374 MET cc_start: 0.6354 (pmm) cc_final: 0.5719 (pmm) REVERT: I 468 MET cc_start: 0.4980 (tmm) cc_final: 0.4067 (tmm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3471 time to fit residues: 63.9782 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 : 1.896 ------------------------------------------------------------------------------- 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: 8.9990 chunk 114 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.039862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031037 restraints weight = 182980.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.031827 restraints weight = 124546.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.032379 restraints weight = 97872.227| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.8162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16083 Z= 0.232 Angle : 0.819 9.680 22047 Z= 0.382 Chirality : 0.050 0.331 2643 Planarity : 0.005 0.058 2619 Dihedral : 8.773 95.867 3738 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.89 (0.19), residues: 1773 helix: 0.16 (0.27), residues: 297 sheet: -0.95 (0.26), residues: 411 loop : -1.86 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 332 HIS 0.004 0.001 HIS C 275 PHE 0.017 0.002 PHE G 259 TYR 0.037 0.002 TYR K 92 ARG 0.008 0.001 ARG B 601 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 42) link_NAG-ASN : angle 2.92238 ( 126) link_ALPHA1-6 : bond 0.01192 ( 6) link_ALPHA1-6 : angle 2.86162 ( 18) link_BETA1-4 : bond 0.00406 ( 30) link_BETA1-4 : angle 2.31267 ( 90) link_ALPHA1-3 : bond 0.00633 ( 9) link_ALPHA1-3 : angle 2.41270 ( 27) hydrogen bonds : bond 0.03865 ( 345) hydrogen bonds : angle 6.33443 ( 927) SS BOND : bond 0.00443 ( 27) SS BOND : angle 1.06035 ( 54) covalent geometry : bond 0.00481 (15969) covalent geometry : angle 0.76914 (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 111 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9613 (tptp) cc_final: 0.9266 (tptt) REVERT: B 588 LYS cc_start: 0.9801 (tmtt) cc_final: 0.9564 (tptp) REVERT: B 639 GLU cc_start: 0.9324 (pp20) cc_final: 0.9112 (pp20) REVERT: B 652 GLN cc_start: 0.9688 (tt0) cc_final: 0.9466 (tm-30) REVERT: G 250 MET cc_start: 0.9206 (mmp) cc_final: 0.8912 (tpp) REVERT: H 60 TYR cc_start: 0.9017 (m-80) cc_final: 0.8749 (m-10) REVERT: H 107 LEU cc_start: 0.9381 (tp) cc_final: 0.9174 (tp) REVERT: A 574 LYS cc_start: 0.9571 (tptt) cc_final: 0.9368 (tptp) REVERT: A 639 GLU cc_start: 0.9384 (pp20) cc_final: 0.9023 (pp20) REVERT: C 250 MET cc_start: 0.9264 (mmp) cc_final: 0.8670 (tpp) REVERT: C 468 MET cc_start: 0.7118 (tmm) cc_final: 0.6472 (tmm) REVERT: D 58 THR cc_start: 0.8038 (p) cc_final: 0.7615 (p) REVERT: D 60 TYR cc_start: 0.8876 (m-80) cc_final: 0.8196 (m-10) REVERT: E 4 MET cc_start: 0.8413 (mmp) cc_final: 0.8126 (mmm) REVERT: F 574 LYS cc_start: 0.9567 (tptp) cc_final: 0.9323 (tptp) REVERT: F 588 LYS cc_start: 0.9737 (tmtt) cc_final: 0.9517 (tptp) REVERT: F 639 GLU cc_start: 0.9340 (pp20) cc_final: 0.9077 (pp20) REVERT: I 374 MET cc_start: 0.7224 (pmm) cc_final: 0.6686 (pmm) REVERT: I 468 MET cc_start: 0.6237 (tmm) cc_final: 0.5796 (ppp) REVERT: K 4 MET cc_start: 0.8778 (mmp) cc_final: 0.8356 (mmm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3741 time to fit residues: 64.1933 Evaluate side-chains 87 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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: 1.9990 chunk 150 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 0.0170 chunk 23 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 157 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- 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** F 590 GLN ** 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 = 0.3256 r_free = 0.3256 target = 0.040548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.031678 restraints weight = 176215.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.032499 restraints weight = 119947.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.033084 restraints weight = 93736.485| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.8207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16083 Z= 0.133 Angle : 0.735 11.083 22047 Z= 0.335 Chirality : 0.049 0.340 2643 Planarity : 0.004 0.049 2619 Dihedral : 8.604 93.381 3738 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.73 (0.20), residues: 1773 helix: 0.31 (0.28), residues: 288 sheet: -0.83 (0.26), residues: 417 loop : -1.75 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 338 HIS 0.002 0.000 HIS C 275 PHE 0.012 0.001 PHE I 236 TYR 0.016 0.001 TYR K 32 ARG 0.004 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 42) link_NAG-ASN : angle 2.75494 ( 126) link_ALPHA1-6 : bond 0.01209 ( 6) link_ALPHA1-6 : angle 2.61408 ( 18) link_BETA1-4 : bond 0.00365 ( 30) link_BETA1-4 : angle 2.22177 ( 90) link_ALPHA1-3 : bond 0.00621 ( 9) link_ALPHA1-3 : angle 2.40622 ( 27) hydrogen bonds : bond 0.03437 ( 345) hydrogen bonds : angle 5.96750 ( 927) SS BOND : bond 0.00330 ( 27) SS BOND : angle 0.68684 ( 54) covalent geometry : bond 0.00285 (15969) covalent geometry : angle 0.68570 (21732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4927.15 seconds wall clock time: 91 minutes 28.37 seconds (5488.37 seconds total)