Starting phenix.real_space_refine on Sun Aug 24 00:26:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dua_27718/08_2025/8dua_27718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dua_27718/08_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_27718/08_2025/8dua_27718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dua_27718/08_2025/8dua_27718.map" model { file = "/net/cci-nas-00/data/ceres_data/8dua_27718/08_2025/8dua_27718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dua_27718/08_2025/8dua_27718.cif" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.05, per 1000 atoms: 0.26 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: 1.49 Conformation dependent library (CDL) restraints added in 642.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.55 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: 2.14 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2539 1.33 - 1.45: 4799 1.45 - 1.58: 8520 1.58 - 1.70: 0 1.70 - 1.83: 111 Bond restraints: 15969 Sorted by residual: bond pdb=" CA ASN G 279 " pdb=" C ASN G 279 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.22e-02 6.72e+03 1.74e+01 bond pdb=" N ARG C 280 " pdb=" CA ARG C 280 " ideal model delta sigma weight residual 1.455 1.500 -0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" N ILE C 282 " pdb=" CA ILE C 282 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.19e-02 7.06e+03 8.80e+00 bond pdb=" N ARG I 280 " pdb=" CA ARG I 280 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.21e+00 bond pdb=" N ASN C 279 " pdb=" CA ASN C 279 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.99e+00 ... (remaining 15964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 21137 2.19 - 4.38: 452 4.38 - 6.57: 130 6.57 - 8.76: 10 8.76 - 10.95: 3 Bond angle restraints: 21732 Sorted by residual: angle pdb=" CA ASN G 279 " pdb=" CB ASN G 279 " pdb=" CG ASN G 279 " ideal model delta sigma weight residual 112.60 101.82 10.78 1.00e+00 1.00e+00 1.16e+02 angle pdb=" N ASN C 279 " pdb=" CA ASN C 279 " pdb=" C ASN C 279 " ideal model delta sigma weight residual 112.72 103.07 9.65 1.14e+00 7.69e-01 7.16e+01 angle pdb=" N ASN I 279 " pdb=" CA ASN I 279 " pdb=" C ASN I 279 " ideal model delta sigma weight residual 112.23 103.86 8.37 1.26e+00 6.30e-01 4.41e+01 angle pdb=" C ASN I 279 " pdb=" CA ASN I 279 " pdb=" CB ASN I 279 " ideal model delta sigma weight residual 110.38 121.33 -10.95 2.04e+00 2.40e-01 2.88e+01 angle pdb=" N THR C 281 " pdb=" CA THR C 281 " pdb=" C THR C 281 " ideal model delta sigma weight residual 109.14 116.65 -7.51 1.49e+00 4.50e-01 2.54e+01 ... (remaining 21727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 9690 24.04 - 48.07: 592 48.07 - 72.11: 110 72.11 - 96.14: 90 96.14 - 120.18: 63 Dihedral angle restraints: 10545 sinusoidal: 5274 harmonic: 5271 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 147.67 -54.67 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual -86.00 -31.80 -54.20 1 1.00e+01 1.00e-02 3.98e+01 ... (remaining 10542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 2585 0.142 - 0.284: 45 0.284 - 0.426: 12 0.426 - 0.568: 0 0.568 - 0.710: 1 Chirality restraints: 2643 Sorted by residual: chirality pdb=" C1 NAG I1008 " pdb=" ND2 ASN I 279 " pdb=" C2 NAG I1008 " pdb=" O5 NAG I1008 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA GLU C 347 " pdb=" N GLU C 347 " pdb=" C GLU C 347 " pdb=" CB GLU C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA GLU I 347 " pdb=" N GLU I 347 " pdb=" C GLU I 347 " pdb=" CB GLU I 347 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 2640 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I1008 " 0.183 2.00e-02 2.50e+03 1.49e-01 2.79e+02 pdb=" C7 NAG I1008 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG I1008 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG I1008 " -0.239 2.00e-02 2.50e+03 pdb=" O7 NAG I1008 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 277 " -0.025 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C LYS G 277 " 0.088 2.00e-02 2.50e+03 pdb=" O LYS G 277 " -0.034 2.00e-02 2.50e+03 pdb=" N SER G 278 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G1008 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG G1008 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G1008 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G1008 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG G1008 " 0.008 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 115 2.49 - 3.09: 11278 3.09 - 3.70: 20916 3.70 - 4.30: 29338 4.30 - 4.90: 47766 Nonbonded interactions: 109413 Sorted by model distance: nonbonded pdb=" O3 NAG C1003 " pdb=" O7 NAG C1003 " model vdw 1.889 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.114 3.040 nonbonded pdb=" OD1 ASN A 612 " pdb=" OG1 THR A 614 " model vdw 2.119 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.131 3.040 nonbonded pdb=" OD1 ASN B 612 " pdb=" OG1 THR B 614 " model vdw 2.133 3.040 ... (remaining 109408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.020 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.980 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 249 TYR 0.007 0.001 TYR C 352C PHE 0.005 0.001 PHE I 53 TRP 0.042 0.001 TRP C 458 HIS 0.009 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00476 (15969) covalent geometry : angle 0.78733 (21732) SS BOND : bond 0.00216 ( 27) SS BOND : angle 0.56683 ( 54) hydrogen bonds : bond 0.34490 ( 345) hydrogen bonds : angle 9.72353 ( 927) link_ALPHA1-3 : bond 0.00586 ( 9) link_ALPHA1-3 : angle 2.16250 ( 27) 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_NAG-ASN : bond 0.01570 ( 42) link_NAG-ASN : angle 5.66998 ( 126) *********************** 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 : 0.636 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: 0.1544 time to fit residues: 55.4356 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 : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 661 GLN G 377 ASN A 661 GLN C 275 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.051815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.041968 restraints weight = 168129.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.042832 restraints weight = 122803.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.043447 restraints weight = 99133.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.043822 restraints weight = 85701.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.044090 restraints weight = 77806.223| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16083 Z= 0.168 Angle : 0.829 10.403 22047 Z= 0.379 Chirality : 0.052 0.389 2643 Planarity : 0.005 0.072 2619 Dihedral : 15.742 111.339 3738 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.19), residues: 1773 helix: -0.35 (0.30), residues: 267 sheet: 0.60 (0.31), residues: 267 loop : -1.64 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.017 0.001 TYR J 90 PHE 0.030 0.002 PHE A 600 TRP 0.012 0.001 TRP C 109 HIS 0.001 0.000 HIS G 352 Details of bonding type rmsd covalent geometry : bond 0.00347 (15969) covalent geometry : angle 0.76687 (21732) SS BOND : bond 0.00396 ( 27) SS BOND : angle 0.82850 ( 54) hydrogen bonds : bond 0.05521 ( 345) hydrogen bonds : angle 7.34047 ( 927) link_ALPHA1-3 : bond 0.00914 ( 9) link_ALPHA1-3 : angle 3.82408 ( 27) link_ALPHA1-6 : bond 0.01011 ( 6) link_ALPHA1-6 : angle 1.89695 ( 18) link_BETA1-4 : bond 0.00480 ( 30) link_BETA1-4 : angle 2.59718 ( 90) link_NAG-ASN : bond 0.00661 ( 42) link_NAG-ASN : angle 3.15820 ( 126) *********************** 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 182 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.502 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: 0.9492 (tt0) cc_final: 0.9068 (tp-100) REVERT: B 639 GLU cc_start: 0.9057 (pp20) cc_final: 0.8829 (pp20) REVERT: B 652 GLN cc_start: 0.9676 (tt0) cc_final: 0.9365 (tm-30) REVERT: G 250 MET cc_start: 0.9085 (mmp) cc_final: 0.8379 (tpp) REVERT: G 468 MET cc_start: 0.3115 (ttp) cc_final: 0.2143 (pmm) REVERT: H 60 TYR cc_start: 0.8830 (m-10) cc_final: 0.8492 (m-80) REVERT: H 72 ASP cc_start: 0.8510 (p0) cc_final: 0.8214 (p0) REVERT: L 10 SER cc_start: 0.9230 (t) cc_final: 0.9015 (p) REVERT: L 54 LEU cc_start: 0.9094 (tp) cc_final: 0.8726 (tt) REVERT: A 652 GLN cc_start: 0.9672 (tt0) cc_final: 0.9260 (tm-30) REVERT: C 468 MET cc_start: 0.3790 (tmm) cc_final: 0.3471 (tmm) REVERT: D 58 THR cc_start: 0.8474 (p) cc_final: 0.8068 (t) REVERT: D 60 TYR cc_start: 0.8645 (m-10) cc_final: 0.8209 (m-80) REVERT: E 94 ASP cc_start: 0.8731 (t0) cc_final: 0.8341 (t70) REVERT: I 479 TYR cc_start: 0.8503 (m-80) cc_final: 0.8220 (m-80) REVERT: J 86 ASP cc_start: 0.7852 (m-30) cc_final: 0.7531 (m-30) REVERT: J 90 TYR cc_start: 0.8781 (m-80) cc_final: 0.8338 (m-80) REVERT: J 107 LEU cc_start: 0.9172 (tp) cc_final: 0.8964 (tp) REVERT: K 30 ASP cc_start: 0.9315 (t70) cc_final: 0.8726 (t0) outliers start: 6 outliers final: 0 residues processed: 179 average time/residue: 0.1320 time to fit residues: 34.0126 Evaluate side-chains 117 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 100 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 82AASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.044296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.034993 restraints weight = 179976.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.035789 restraints weight = 127651.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.036333 restraints weight = 101982.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.036722 restraints weight = 88101.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.036965 restraints weight = 79560.730| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 16083 Z= 0.302 Angle : 0.941 9.917 22047 Z= 0.452 Chirality : 0.053 0.356 2643 Planarity : 0.006 0.088 2619 Dihedral : 12.228 116.824 3738 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.56 % Allowed : 5.15 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.18), residues: 1773 helix: -0.85 (0.27), residues: 300 sheet: -0.36 (0.26), residues: 330 loop : -2.00 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 24 TYR 0.041 0.003 TYR B 586 PHE 0.020 0.003 PHE L 62 TRP 0.034 0.003 TRP F 610 HIS 0.005 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00636 (15969) covalent geometry : angle 0.89141 (21732) SS BOND : bond 0.00521 ( 27) SS BOND : angle 1.09175 ( 54) hydrogen bonds : bond 0.05282 ( 345) hydrogen bonds : angle 7.03508 ( 927) link_ALPHA1-3 : bond 0.01253 ( 9) link_ALPHA1-3 : angle 2.44656 ( 27) link_ALPHA1-6 : bond 0.01543 ( 6) link_ALPHA1-6 : angle 3.91179 ( 18) link_BETA1-4 : bond 0.00543 ( 30) link_BETA1-4 : angle 2.45444 ( 90) link_NAG-ASN : bond 0.00833 ( 42) link_NAG-ASN : angle 3.10703 ( 126) *********************** 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 142 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 587 LEU cc_start: 0.9712 (pt) cc_final: 0.9499 (pt) REVERT: B 633 ARG cc_start: 0.8825 (mtm110) cc_final: 0.8603 (mtm180) REVERT: B 652 GLN cc_start: 0.9716 (tt0) cc_final: 0.9449 (tm-30) REVERT: G 250 MET cc_start: 0.9316 (mmp) cc_final: 0.8862 (tpp) REVERT: G 468 MET cc_start: 0.5606 (tmm) cc_final: 0.5129 (ppp) REVERT: H 58 THR cc_start: 0.6633 (t) cc_final: 0.5982 (t) REVERT: A 583 ILE cc_start: 0.9799 (OUTLIER) cc_final: 0.9578 (tp) REVERT: A 652 GLN cc_start: 0.9695 (tt0) cc_final: 0.9331 (tm-30) REVERT: C 468 MET cc_start: 0.5633 (tmm) cc_final: 0.5197 (ppp) REVERT: D 58 THR cc_start: 0.8735 (p) cc_final: 0.7809 (p) REVERT: F 583 ILE cc_start: 0.9785 (OUTLIER) cc_final: 0.9473 (tp) REVERT: I 374 MET cc_start: 0.5659 (pmm) cc_final: 0.4934 (pmm) REVERT: J 107 LEU cc_start: 0.9324 (tp) cc_final: 0.9097 (tp) outliers start: 9 outliers final: 1 residues processed: 138 average time/residue: 0.1322 time to fit residues: 26.8399 Evaluate side-chains 101 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 109 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 122 optimal weight: 0.2980 chunk 130 optimal weight: 0.0970 chunk 137 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 86 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** ** 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 = 0.3419 r_free = 0.3419 target = 0.046362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.036768 restraints weight = 171772.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.037574 restraints weight = 123296.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.038167 restraints weight = 99549.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.038519 restraints weight = 86204.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.038807 restraints weight = 78656.415| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5027 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= 0.129 Angle : 0.763 11.444 22047 Z= 0.344 Chirality : 0.051 0.348 2643 Planarity : 0.004 0.039 2619 Dihedral : 11.036 111.646 3738 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.13 % Allowed : 2.32 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.18), residues: 1773 helix: -0.55 (0.27), residues: 291 sheet: -0.34 (0.27), residues: 321 loop : -1.78 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 295 TYR 0.019 0.001 TYR B 658 PHE 0.012 0.001 PHE K 49 TRP 0.015 0.001 TRP F 610 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd covalent geometry : bond 0.00262 (15969) covalent geometry : angle 0.71091 (21732) SS BOND : bond 0.00252 ( 27) SS BOND : angle 0.73152 ( 54) hydrogen bonds : bond 0.04032 ( 345) hydrogen bonds : angle 6.16736 ( 927) link_ALPHA1-3 : bond 0.01036 ( 9) link_ALPHA1-3 : angle 3.14089 ( 27) link_ALPHA1-6 : bond 0.01565 ( 6) link_ALPHA1-6 : angle 2.47385 ( 18) link_BETA1-4 : bond 0.00383 ( 30) link_BETA1-4 : angle 2.22141 ( 90) link_NAG-ASN : bond 0.00602 ( 42) link_NAG-ASN : angle 2.83770 ( 126) *********************** 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 138 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9518 (tptp) cc_final: 0.9162 (tptp) REVERT: B 588 LYS cc_start: 0.9749 (tmtt) cc_final: 0.9486 (tptp) REVERT: B 639 GLU cc_start: 0.9109 (pp20) cc_final: 0.8854 (pp20) REVERT: B 652 GLN cc_start: 0.9687 (tt0) cc_final: 0.9415 (tm-30) REVERT: G 250 MET cc_start: 0.9307 (mmp) cc_final: 0.8712 (tpp) REVERT: G 468 MET cc_start: 0.6397 (tmm) cc_final: 0.5660 (ppp) REVERT: H 58 THR cc_start: 0.5717 (t) cc_final: 0.5198 (t) REVERT: A 587 LEU cc_start: 0.9503 (pp) cc_final: 0.9142 (pp) REVERT: A 639 GLU cc_start: 0.9182 (pp20) cc_final: 0.8870 (pp20) REVERT: A 652 GLN cc_start: 0.9665 (tt0) cc_final: 0.9302 (tm-30) REVERT: C 250 MET cc_start: 0.9331 (mmp) cc_final: 0.8692 (tpp) REVERT: C 374 MET cc_start: 0.7442 (pmm) cc_final: 0.7224 (pmm) REVERT: C 468 MET cc_start: 0.5684 (tmm) cc_final: 0.5437 (tmm) REVERT: D 58 THR cc_start: 0.7990 (p) cc_final: 0.6798 (p) REVERT: D 60 TYR cc_start: 0.8460 (m-80) cc_final: 0.7914 (m-10) REVERT: E 4 MET cc_start: 0.6911 (mmp) cc_final: 0.6675 (mmm) REVERT: E 70 LYS cc_start: 0.9059 (mmpt) cc_final: 0.8833 (mmmt) REVERT: F 583 ILE cc_start: 0.9710 (OUTLIER) cc_final: 0.9334 (tp) REVERT: F 639 GLU cc_start: 0.9069 (pp20) cc_final: 0.8771 (pp20) REVERT: I 468 MET cc_start: 0.2319 (tmm) cc_final: 0.1958 (tmm) REVERT: J 107 LEU cc_start: 0.9179 (tp) cc_final: 0.8965 (tp) REVERT: K 30 ASP cc_start: 0.9317 (t70) cc_final: 0.8648 (t0) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.1375 time to fit residues: 27.6514 Evaluate side-chains 102 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN D 39 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.044076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.034778 restraints weight = 177112.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.035569 restraints weight = 126704.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.036127 restraints weight = 102185.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.036453 restraints weight = 88433.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.036723 restraints weight = 80705.028| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16083 Z= 0.181 Angle : 0.756 9.795 22047 Z= 0.347 Chirality : 0.049 0.342 2643 Planarity : 0.004 0.034 2619 Dihedral : 9.975 111.880 3738 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.19 % Allowed : 2.95 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.18), residues: 1773 helix: -0.32 (0.27), residues: 291 sheet: -0.34 (0.27), residues: 324 loop : -1.86 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 24 TYR 0.018 0.002 TYR F 586 PHE 0.014 0.001 PHE L 62 TRP 0.017 0.001 TRP F 610 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00378 (15969) covalent geometry : angle 0.70427 (21732) SS BOND : bond 0.00376 ( 27) SS BOND : angle 0.77704 ( 54) hydrogen bonds : bond 0.03958 ( 345) hydrogen bonds : angle 6.16788 ( 927) link_ALPHA1-3 : bond 0.01128 ( 9) link_ALPHA1-3 : angle 2.81828 ( 27) link_ALPHA1-6 : bond 0.01845 ( 6) link_ALPHA1-6 : angle 3.00277 ( 18) link_BETA1-4 : bond 0.00421 ( 30) link_BETA1-4 : angle 2.11836 ( 90) link_NAG-ASN : bond 0.00658 ( 42) link_NAG-ASN : angle 2.84524 ( 126) *********************** 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 130 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9568 (tptp) cc_final: 0.9240 (tptp) REVERT: B 588 LYS cc_start: 0.9816 (tmtt) cc_final: 0.9557 (tptp) REVERT: B 633 ARG cc_start: 0.8705 (mtm110) cc_final: 0.8466 (mtm180) REVERT: B 639 GLU cc_start: 0.9280 (pp20) cc_final: 0.9021 (pp20) REVERT: B 652 GLN cc_start: 0.9716 (tt0) cc_final: 0.9429 (tm-30) REVERT: G 250 MET cc_start: 0.9316 (mmp) cc_final: 0.8757 (tpp) REVERT: G 468 MET cc_start: 0.6170 (tmm) cc_final: 0.5581 (ppp) REVERT: H 60 TYR cc_start: 0.8730 (m-80) cc_final: 0.8398 (m-10) REVERT: A 639 GLU cc_start: 0.9301 (pp20) cc_final: 0.8905 (pp20) REVERT: A 652 GLN cc_start: 0.9699 (tt0) cc_final: 0.9360 (tm-30) REVERT: C 250 MET cc_start: 0.9359 (mmp) cc_final: 0.8823 (tpp) REVERT: C 468 MET cc_start: 0.6095 (tmm) cc_final: 0.5630 (ppp) REVERT: D 58 THR cc_start: 0.8099 (p) cc_final: 0.6993 (p) REVERT: D 60 TYR cc_start: 0.8622 (m-80) cc_final: 0.7991 (m-10) REVERT: E 4 MET cc_start: 0.7435 (mmp) cc_final: 0.7078 (mmm) REVERT: F 583 ILE cc_start: 0.9765 (OUTLIER) cc_final: 0.9395 (tp) REVERT: F 639 GLU cc_start: 0.9232 (pp20) cc_final: 0.8917 (pp20) REVERT: I 468 MET cc_start: 0.2706 (tmm) cc_final: 0.2284 (tmm) REVERT: J 82 ASN cc_start: 0.8411 (p0) cc_final: 0.7804 (t0) REVERT: J 107 LEU cc_start: 0.9293 (tp) cc_final: 0.9064 (tp) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.1389 time to fit residues: 26.7687 Evaluate side-chains 97 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 130 optimal weight: 0.4980 chunk 156 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** C 254 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** ** 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 = 0.3371 r_free = 0.3371 target = 0.044694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035371 restraints weight = 174371.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.036186 restraints weight = 124245.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.036752 restraints weight = 99781.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.037133 restraints weight = 86398.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.037374 restraints weight = 78214.807| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5818 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= 0.126 Angle : 0.721 9.864 22047 Z= 0.325 Chirality : 0.049 0.347 2643 Planarity : 0.004 0.033 2619 Dihedral : 9.538 111.101 3738 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.06 % Allowed : 1.51 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.19), residues: 1773 helix: -0.19 (0.27), residues: 291 sheet: -0.26 (0.27), residues: 324 loop : -1.76 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.012 0.001 TYR L 32 PHE 0.011 0.001 PHE B 600 TRP 0.011 0.001 TRP C 338 HIS 0.002 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00259 (15969) covalent geometry : angle 0.66352 (21732) SS BOND : bond 0.00268 ( 27) SS BOND : angle 0.62053 ( 54) hydrogen bonds : bond 0.03679 ( 345) hydrogen bonds : angle 5.98531 ( 927) link_ALPHA1-3 : bond 0.00966 ( 9) link_ALPHA1-3 : angle 2.82236 ( 27) link_ALPHA1-6 : bond 0.01781 ( 6) link_ALPHA1-6 : angle 3.13765 ( 18) link_BETA1-4 : bond 0.00404 ( 30) link_BETA1-4 : angle 2.09624 ( 90) link_NAG-ASN : bond 0.00573 ( 42) link_NAG-ASN : angle 2.93790 ( 126) *********************** 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 129 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9570 (tptp) cc_final: 0.9217 (tptp) REVERT: B 588 LYS cc_start: 0.9810 (tmtt) cc_final: 0.9566 (tptp) REVERT: B 639 GLU cc_start: 0.9260 (pp20) cc_final: 0.8986 (pp20) REVERT: B 652 GLN cc_start: 0.9700 (tt0) cc_final: 0.9432 (tm-30) REVERT: G 250 MET cc_start: 0.9321 (mmp) cc_final: 0.8764 (tpp) REVERT: G 468 MET cc_start: 0.6523 (tmm) cc_final: 0.5962 (ppp) REVERT: H 58 THR cc_start: 0.6581 (t) cc_final: 0.6216 (t) REVERT: H 60 TYR cc_start: 0.8672 (m-80) cc_final: 0.8379 (m-10) REVERT: A 600 PHE cc_start: 0.7227 (m-80) cc_final: 0.6995 (m-80) REVERT: A 639 GLU cc_start: 0.9294 (pp20) cc_final: 0.8911 (pp20) REVERT: A 652 GLN cc_start: 0.9683 (tt0) cc_final: 0.9349 (tm-30) REVERT: C 250 MET cc_start: 0.9376 (mmp) cc_final: 0.8686 (tpp) REVERT: C 468 MET cc_start: 0.6081 (tmm) cc_final: 0.5650 (ppp) REVERT: D 58 THR cc_start: 0.8073 (p) cc_final: 0.7059 (p) REVERT: D 60 TYR cc_start: 0.8605 (m-80) cc_final: 0.7972 (m-10) REVERT: E 4 MET cc_start: 0.7342 (mmp) cc_final: 0.7133 (mmm) REVERT: F 639 GLU cc_start: 0.9191 (pp20) cc_final: 0.8889 (pp20) REVERT: I 468 MET cc_start: 0.2965 (tmm) cc_final: 0.2556 (tmm) REVERT: J 82 ASN cc_start: 0.8383 (p0) cc_final: 0.7784 (t0) REVERT: J 107 LEU cc_start: 0.9255 (tp) cc_final: 0.9038 (tp) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1266 time to fit residues: 25.0793 Evaluate side-chains 100 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 37 optimal weight: 0.0470 chunk 173 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 0.6092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 39 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.045177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.035760 restraints weight = 169928.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.036614 restraints weight = 120412.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.037164 restraints weight = 96174.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.037568 restraints weight = 83008.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.037837 restraints weight = 74943.179| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16083 Z= 0.114 Angle : 0.717 13.206 22047 Z= 0.320 Chirality : 0.049 0.345 2643 Planarity : 0.004 0.039 2619 Dihedral : 9.115 109.857 3738 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.06 % Allowed : 1.07 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.19), residues: 1773 helix: -0.03 (0.28), residues: 291 sheet: 0.04 (0.28), residues: 300 loop : -1.73 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.023 0.001 TYR B 586 PHE 0.017 0.001 PHE B 600 TRP 0.010 0.001 TRP D 36 HIS 0.002 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00231 (15969) covalent geometry : angle 0.66118 (21732) SS BOND : bond 0.00314 ( 27) SS BOND : angle 0.68339 ( 54) hydrogen bonds : bond 0.03448 ( 345) hydrogen bonds : angle 5.71991 ( 927) link_ALPHA1-3 : bond 0.00865 ( 9) link_ALPHA1-3 : angle 2.72299 ( 27) link_ALPHA1-6 : bond 0.01665 ( 6) link_ALPHA1-6 : angle 3.17138 ( 18) link_BETA1-4 : bond 0.00442 ( 30) link_BETA1-4 : angle 2.04486 ( 90) link_NAG-ASN : bond 0.00609 ( 42) link_NAG-ASN : angle 2.88296 ( 126) *********************** 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 132 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9586 (tptp) cc_final: 0.9220 (tptp) REVERT: B 588 LYS cc_start: 0.9820 (tmtt) cc_final: 0.9547 (tptp) REVERT: B 639 GLU cc_start: 0.9288 (pp20) cc_final: 0.8983 (pp20) REVERT: B 652 GLN cc_start: 0.9715 (tt0) cc_final: 0.9409 (tm-30) REVERT: G 250 MET cc_start: 0.9341 (mmp) cc_final: 0.8745 (tpp) REVERT: G 468 MET cc_start: 0.6203 (tmm) cc_final: 0.5502 (ppp) REVERT: A 584 GLU cc_start: 0.9313 (pp20) cc_final: 0.9072 (pp20) REVERT: A 639 GLU cc_start: 0.9331 (pp20) cc_final: 0.8938 (pp20) REVERT: A 652 GLN cc_start: 0.9664 (tt0) cc_final: 0.9284 (tm-30) REVERT: C 250 MET cc_start: 0.9374 (mmp) cc_final: 0.8649 (tpp) REVERT: C 468 MET cc_start: 0.6072 (tmm) cc_final: 0.5583 (ppp) REVERT: D 58 THR cc_start: 0.8212 (p) cc_final: 0.7298 (p) REVERT: D 60 TYR cc_start: 0.8668 (m-80) cc_final: 0.8053 (m-10) REVERT: F 639 GLU cc_start: 0.9178 (pp20) cc_final: 0.8904 (pp20) REVERT: I 468 MET cc_start: 0.2947 (tmm) cc_final: 0.2491 (tmm) REVERT: J 82 ASN cc_start: 0.8412 (p0) cc_final: 0.7859 (t0) REVERT: J 107 LEU cc_start: 0.9247 (tp) cc_final: 0.9042 (tp) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1297 time to fit residues: 26.1633 Evaluate side-chains 102 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 106 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 71 optimal weight: 40.0000 chunk 18 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 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 = 0.3327 r_free = 0.3327 target = 0.043089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.033894 restraints weight = 177807.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.034675 restraints weight = 125068.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.035254 restraints weight = 100239.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.035610 restraints weight = 86074.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.035917 restraints weight = 77950.859| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16083 Z= 0.176 Angle : 0.751 9.647 22047 Z= 0.344 Chirality : 0.049 0.341 2643 Planarity : 0.004 0.040 2619 Dihedral : 8.926 107.918 3738 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.13 % Allowed : 1.07 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.19), residues: 1773 helix: 0.04 (0.28), residues: 291 sheet: -0.49 (0.27), residues: 360 loop : -1.66 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.020 0.002 TYR B 586 PHE 0.013 0.002 PHE B 600 TRP 0.020 0.001 TRP B 610 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00370 (15969) covalent geometry : angle 0.69876 (21732) SS BOND : bond 0.00341 ( 27) SS BOND : angle 0.73647 ( 54) hydrogen bonds : bond 0.03692 ( 345) hydrogen bonds : angle 6.05767 ( 927) link_ALPHA1-3 : bond 0.00829 ( 9) link_ALPHA1-3 : angle 2.60334 ( 27) link_ALPHA1-6 : bond 0.01533 ( 6) link_ALPHA1-6 : angle 3.17453 ( 18) link_BETA1-4 : bond 0.00360 ( 30) link_BETA1-4 : angle 2.08047 ( 90) link_NAG-ASN : bond 0.00645 ( 42) link_NAG-ASN : angle 2.87842 ( 126) *********************** 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 126 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9555 (tptp) cc_final: 0.9265 (tptp) REVERT: B 588 LYS cc_start: 0.9795 (tmtt) cc_final: 0.9550 (tptp) REVERT: B 639 GLU cc_start: 0.9216 (pp20) cc_final: 0.9002 (pp20) REVERT: G 250 MET cc_start: 0.9307 (mmp) cc_final: 0.8799 (tpp) REVERT: G 468 MET cc_start: 0.6403 (tmm) cc_final: 0.5686 (ppp) REVERT: A 639 GLU cc_start: 0.9327 (pp20) cc_final: 0.8966 (pp20) REVERT: C 250 MET cc_start: 0.9342 (mmp) cc_final: 0.8686 (tpp) REVERT: C 468 MET cc_start: 0.5817 (tmm) cc_final: 0.5212 (ppp) REVERT: D 58 THR cc_start: 0.7866 (p) cc_final: 0.6960 (p) REVERT: D 60 TYR cc_start: 0.8492 (m-80) cc_final: 0.8006 (m-10) REVERT: F 639 GLU cc_start: 0.9188 (pp20) cc_final: 0.8910 (pp20) REVERT: I 374 MET cc_start: 0.6294 (pmm) cc_final: 0.5955 (pmm) REVERT: I 468 MET cc_start: 0.3647 (tmm) cc_final: 0.3051 (tmm) outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.1291 time to fit residues: 24.5032 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 : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 166 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 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 = 0.3347 r_free = 0.3347 target = 0.043684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.034490 restraints weight = 173877.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.035316 restraints weight = 123382.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.035869 restraints weight = 98521.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.036272 restraints weight = 84903.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.036528 restraints weight = 76461.518| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16083 Z= 0.121 Angle : 0.715 11.429 22047 Z= 0.323 Chirality : 0.049 0.341 2643 Planarity : 0.004 0.034 2619 Dihedral : 8.747 106.594 3738 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.19), residues: 1773 helix: 0.08 (0.28), residues: 291 sheet: -0.42 (0.27), residues: 360 loop : -1.61 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.011 0.001 TYR L 32 PHE 0.009 0.001 PHE C 236 TRP 0.013 0.001 TRP G 332 HIS 0.002 0.000 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00255 (15969) covalent geometry : angle 0.66021 (21732) SS BOND : bond 0.00286 ( 27) SS BOND : angle 0.63394 ( 54) hydrogen bonds : bond 0.03402 ( 345) hydrogen bonds : angle 5.80143 ( 927) link_ALPHA1-3 : bond 0.00803 ( 9) link_ALPHA1-3 : angle 2.58982 ( 27) link_ALPHA1-6 : bond 0.01448 ( 6) link_ALPHA1-6 : angle 3.00763 ( 18) link_BETA1-4 : bond 0.00387 ( 30) link_BETA1-4 : angle 2.06505 ( 90) link_NAG-ASN : bond 0.00583 ( 42) link_NAG-ASN : angle 2.86923 ( 126) *********************** 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 127 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9581 (tptp) cc_final: 0.9268 (tptp) REVERT: B 588 LYS cc_start: 0.9799 (tmtt) cc_final: 0.9528 (tptp) REVERT: B 639 GLU cc_start: 0.9244 (pp20) cc_final: 0.8982 (pp20) REVERT: G 250 MET cc_start: 0.9316 (mmp) cc_final: 0.8775 (tpp) REVERT: G 468 MET cc_start: 0.5775 (tmm) cc_final: 0.5411 (ppp) REVERT: A 639 GLU cc_start: 0.9319 (pp20) cc_final: 0.8970 (pp20) REVERT: C 250 MET cc_start: 0.9328 (mmp) cc_final: 0.8653 (tpp) REVERT: C 468 MET cc_start: 0.6033 (tmm) cc_final: 0.5440 (ppp) REVERT: D 58 THR cc_start: 0.8194 (p) cc_final: 0.7323 (p) REVERT: D 60 TYR cc_start: 0.8571 (m-80) cc_final: 0.8048 (m-10) REVERT: F 639 GLU cc_start: 0.9143 (pp20) cc_final: 0.8889 (pp20) REVERT: I 374 MET cc_start: 0.6180 (pmm) cc_final: 0.5799 (pmm) REVERT: I 468 MET cc_start: 0.3709 (tmm) cc_final: 0.3140 (tmm) REVERT: J 82 ASN cc_start: 0.8319 (p0) cc_final: 0.7706 (t0) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1241 time to fit residues: 23.9619 Evaluate side-chains 93 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 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 = 0.3252 r_free = 0.3252 target = 0.040554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.031774 restraints weight = 182925.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.032553 restraints weight = 128260.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.033094 restraints weight = 101933.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.033419 restraints weight = 87396.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.033679 restraints weight = 79417.005| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.7685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 16083 Z= 0.248 Angle : 0.839 9.769 22047 Z= 0.397 Chirality : 0.050 0.334 2643 Planarity : 0.005 0.067 2619 Dihedral : 8.871 102.470 3738 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.13 % Allowed : 0.50 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.19), residues: 1773 helix: -0.14 (0.27), residues: 297 sheet: -0.92 (0.26), residues: 396 loop : -1.82 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 601 TYR 0.028 0.003 TYR B 586 PHE 0.017 0.002 PHE G 259 TRP 0.021 0.002 TRP J 33 HIS 0.004 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00513 (15969) covalent geometry : angle 0.79009 (21732) SS BOND : bond 0.01789 ( 27) SS BOND : angle 1.21024 ( 54) hydrogen bonds : bond 0.04002 ( 345) hydrogen bonds : angle 6.35499 ( 927) link_ALPHA1-3 : bond 0.00666 ( 9) link_ALPHA1-3 : angle 2.46163 ( 27) link_ALPHA1-6 : bond 0.01245 ( 6) link_ALPHA1-6 : angle 3.01710 ( 18) link_BETA1-4 : bond 0.00438 ( 30) link_BETA1-4 : angle 2.30687 ( 90) link_NAG-ASN : bond 0.00771 ( 42) link_NAG-ASN : angle 2.90351 ( 126) ********************** 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 115 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9592 (tptp) cc_final: 0.9253 (tptt) REVERT: B 588 LYS cc_start: 0.9815 (tmtt) cc_final: 0.9578 (tptp) REVERT: B 639 GLU cc_start: 0.9255 (pp20) cc_final: 0.9054 (pp20) REVERT: B 652 GLN cc_start: 0.9690 (tt0) cc_final: 0.9455 (tm-30) REVERT: G 250 MET cc_start: 0.9175 (mmp) cc_final: 0.8882 (tpp) REVERT: A 639 GLU cc_start: 0.9367 (pp20) cc_final: 0.9035 (pp20) REVERT: C 250 MET cc_start: 0.9224 (mmp) cc_final: 0.8868 (tpp) REVERT: C 468 MET cc_start: 0.6622 (tmm) cc_final: 0.5816 (ppp) REVERT: D 58 THR cc_start: 0.8021 (p) cc_final: 0.7560 (p) REVERT: D 60 TYR cc_start: 0.8688 (m-80) cc_final: 0.8195 (m-80) REVERT: F 639 GLU cc_start: 0.9310 (pp20) cc_final: 0.9012 (pp20) REVERT: I 374 MET cc_start: 0.6495 (pmm) cc_final: 0.6074 (pmm) REVERT: I 468 MET cc_start: 0.5424 (tmm) cc_final: 0.4674 (ppp) REVERT: J 60 TYR cc_start: 0.9153 (m-80) cc_final: 0.8946 (m-80) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.1374 time to fit residues: 23.7311 Evaluate side-chains 85 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 166 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 80 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.042092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.032934 restraints weight = 175272.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.033773 restraints weight = 121168.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.034372 restraints weight = 95598.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.034779 restraints weight = 81089.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.034994 restraints weight = 72674.098| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.7591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16083 Z= 0.118 Angle : 0.743 13.557 22047 Z= 0.337 Chirality : 0.049 0.340 2643 Planarity : 0.004 0.048 2619 Dihedral : 8.613 100.191 3738 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.06 % Allowed : 0.13 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.20), residues: 1773 helix: 0.03 (0.28), residues: 288 sheet: -0.59 (0.27), residues: 411 loop : -1.65 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 633 TYR 0.029 0.001 TYR F 586 PHE 0.011 0.001 PHE C 236 TRP 0.019 0.001 TRP I 338 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00250 (15969) covalent geometry : angle 0.69416 (21732) SS BOND : bond 0.00282 ( 27) SS BOND : angle 0.75363 ( 54) hydrogen bonds : bond 0.03444 ( 345) hydrogen bonds : angle 5.86646 ( 927) link_ALPHA1-3 : bond 0.00588 ( 9) link_ALPHA1-3 : angle 2.47538 ( 27) link_ALPHA1-6 : bond 0.01360 ( 6) link_ALPHA1-6 : angle 2.73505 ( 18) link_BETA1-4 : bond 0.00370 ( 30) link_BETA1-4 : angle 2.17287 ( 90) link_NAG-ASN : bond 0.00590 ( 42) link_NAG-ASN : angle 2.74001 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.44 seconds wall clock time: 40 minutes 42.05 seconds (2442.05 seconds total)