Starting phenix.real_space_refine on Fri Jul 3 19:02:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dua_27718/07_2026/8dua_27718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dua_27718/07_2026/8dua_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dua_27718/07_2026/8dua_27718.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dua_27718/07_2026/8dua_27718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dua_27718/07_2026/8dua_27718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dua_27718/07_2026/8dua_27718.map" model { file = "/net/cci-nas-00/data/ceres_data/8dua_27718/07_2026/8dua_27718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dua_27718/07_2026/8dua_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 3.58, per 1000 atoms: 0.23 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: 1.96 Conformation dependent library (CDL) restraints added in 752.3 milliseconds 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: 0.45 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: 2.29 Time building geometry restraints manager: 2.44 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 - 14.68: 7681 14.68 - 29.36: 770 29.36 - 44.04: 243 44.04 - 58.72: 57 58.72 - 73.40: 27 Dihedral angle restraints: 8778 sinusoidal: 3507 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 8775 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.370 Find NCS groups from input model: 0.370 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 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 : 13.406 73.397 5307 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 are 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/Z covalent geometry : bond 0.00476 / 0.25 (15969) covalent geometry : angle 0.78733 / 0.37 (21732) SS BOND : bond 0.00216 / 0.13 ( 27) SS BOND : angle 0.56683 / 0.41 ( 54) hydrogen bonds : bond 0.34490 / 22.64 ( 345) hydrogen bonds : angle 9.72353 / 6.90 ( 927) link_ALPHA1-3 : bond 0.00586 / 0.31 ( 9) link_ALPHA1-3 : angle 2.16250 / 1.42 ( 27) link_ALPHA1-6 : bond 0.00469 / 0.25 ( 6) link_ALPHA1-6 : angle 1.57227 / 0.92 ( 18) link_BETA1-4 : bond 0.00482 / 0.32 ( 30) link_BETA1-4 : angle 1.88975 / 1.31 ( 90) link_NAG-ASN : bond 0.01570 / 1.22 ( 42) link_NAG-ASN : angle 5.66998 / 3.66 ( 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 : 0.588 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: 0.1540 time to fit residues: 55.6069 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 : 0.589 ------------------------------------------------------------------------------- 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... B 661 GLN G 377 ASN A 661 GLN C 377 ASN F 594 ASN F 661 GLN I 377 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.052045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.042157 restraints weight = 167456.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.043033 restraints weight = 122617.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.043640 restraints weight = 98909.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.044060 restraints weight = 85468.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.044329 restraints weight = 76938.311| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16083 Z= 0.167 Angle : 0.765 10.368 22047 Z= 0.363 Chirality : 0.048 0.383 2643 Planarity : 0.005 0.051 2619 Dihedral : 4.355 17.605 1971 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 0.25 % Allowed : 2.76 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.19), residues: 1773 helix: -0.29 (0.31), residues: 264 sheet: 0.58 (0.30), residues: 273 loop : -1.65 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 81 TYR 0.040 0.002 TYR J 90 PHE 0.030 0.002 PHE A 600 TRP 0.013 0.001 TRP C 458 HIS 0.002 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (15969) covalent geometry : angle 0.71585 / 0.35 (21732) SS BOND : bond 0.00364 / 0.24 ( 27) SS BOND : angle 0.72014 / 0.53 ( 54) hydrogen bonds : bond 0.06120 / 3.84 ( 345) hydrogen bonds : angle 7.54105 / 5.34 ( 927) link_ALPHA1-3 : bond 0.00678 / 0.36 ( 9) link_ALPHA1-3 : angle 2.26655 / 1.51 ( 27) link_ALPHA1-6 : bond 0.00390 / 0.20 ( 6) link_ALPHA1-6 : angle 1.45330 / 0.85 ( 18) link_BETA1-4 : bond 0.00448 / 0.29 ( 30) link_BETA1-4 : angle 2.03654 / 1.50 ( 90) link_NAG-ASN : bond 0.00625 / 0.35 ( 42) link_NAG-ASN : angle 3.09190 / 2.38 ( 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 173 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 169 time to evaluate : 0.605 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: B 577 GLN cc_start: 0.9490 (tt0) cc_final: 0.9089 (tp-100) REVERT: B 639 GLU cc_start: 0.9037 (pp20) cc_final: 0.8829 (pp20) REVERT: B 652 GLN cc_start: 0.9661 (tt0) cc_final: 0.9351 (tm-30) REVERT: G 250 MET cc_start: 0.9043 (mmp) cc_final: 0.8344 (tpp) REVERT: G 468 MET cc_start: 0.3018 (ttp) cc_final: 0.2066 (pmm) REVERT: H 58 THR cc_start: 0.7706 (p) cc_final: 0.7429 (p) REVERT: H 72 ASP cc_start: 0.8462 (p0) cc_final: 0.8127 (p0) REVERT: L 10 SER cc_start: 0.9204 (t) cc_final: 0.8987 (p) REVERT: L 54 LEU cc_start: 0.9070 (tp) cc_final: 0.8706 (tt) REVERT: A 652 GLN cc_start: 0.9675 (tt0) cc_final: 0.9253 (tm-30) REVERT: C 468 MET cc_start: 0.3383 (tmm) cc_final: 0.3041 (tmm) REVERT: D 58 THR cc_start: 0.8532 (p) cc_final: 0.8162 (t) REVERT: D 60 TYR cc_start: 0.8649 (m-10) cc_final: 0.8215 (m-80) REVERT: E 94 ASP cc_start: 0.8707 (t0) cc_final: 0.8312 (t70) REVERT: F 577 GLN cc_start: 0.9382 (tt0) cc_final: 0.9177 (tm-30) REVERT: F 639 GLU cc_start: 0.8850 (pp20) cc_final: 0.8633 (pp20) REVERT: I 479 TYR cc_start: 0.8467 (m-80) cc_final: 0.8237 (m-80) REVERT: J 86 ASP cc_start: 0.7845 (m-30) cc_final: 0.7539 (m-30) REVERT: J 90 TYR cc_start: 0.8730 (m-80) cc_final: 0.8303 (m-80) REVERT: J 107 LEU cc_start: 0.9153 (tp) cc_final: 0.8934 (tp) REVERT: K 30 ASP cc_start: 0.9314 (t70) cc_final: 0.8726 (t0) outliers start: 4 outliers final: 0 residues processed: 170 average time/residue: 0.1334 time to fit residues: 33.5812 Evaluate side-chains 121 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 0.9980 chunk 128 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 GLN H 3 GLN C 73 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.046582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.037039 restraints weight = 176454.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.037853 restraints weight = 126174.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.038426 restraints weight = 101371.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.038790 restraints weight = 87480.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.039075 restraints weight = 79267.260| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16083 Z= 0.239 Angle : 0.806 24.956 22047 Z= 0.383 Chirality : 0.047 0.332 2643 Planarity : 0.005 0.079 2619 Dihedral : 4.867 21.034 1971 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.31 % Allowed : 4.39 % Favored : 95.29 % 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 are not related in a simple way. whole: -1.88 (0.18), residues: 1773 helix: -0.50 (0.27), residues: 300 sheet: -0.10 (0.27), residues: 324 loop : -1.91 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.030 0.002 TYR B 586 PHE 0.017 0.002 PHE L 62 TRP 0.026 0.002 TRP F 610 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 (15969) covalent geometry : angle 0.76702 / 0.37 (21732) SS BOND : bond 0.00397 / 0.26 ( 27) SS BOND : angle 0.98271 / 0.70 ( 54) hydrogen bonds : bond 0.04575 / 2.92 ( 345) hydrogen bonds : angle 6.81099 / 4.85 ( 927) link_ALPHA1-3 : bond 0.00766 / 0.38 ( 9) link_ALPHA1-3 : angle 1.94226 / 1.29 ( 27) link_ALPHA1-6 : bond 0.00212 / 0.09 ( 6) link_ALPHA1-6 : angle 1.36632 / 0.78 ( 18) link_BETA1-4 : bond 0.00477 / 0.28 ( 30) link_BETA1-4 : angle 1.88674 / 1.33 ( 90) link_NAG-ASN : bond 0.00653 / 0.39 ( 42) link_NAG-ASN : angle 2.85458 / 2.27 ( 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 145 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9523 (tptp) cc_final: 0.9173 (tptp) REVERT: B 583 ILE cc_start: 0.9786 (OUTLIER) cc_final: 0.9481 (tp) REVERT: B 588 LYS cc_start: 0.9735 (tmtt) cc_final: 0.9535 (tptp) REVERT: B 652 GLN cc_start: 0.9678 (tt0) cc_final: 0.9409 (tm-30) REVERT: G 250 MET cc_start: 0.9343 (mmp) cc_final: 0.8705 (tpp) REVERT: G 468 MET cc_start: 0.5573 (tmm) cc_final: 0.5024 (tmm) REVERT: H 72 ASP cc_start: 0.8810 (p0) cc_final: 0.8445 (p0) REVERT: A 587 LEU cc_start: 0.9535 (pp) cc_final: 0.9276 (pp) REVERT: A 652 GLN cc_start: 0.9649 (tt0) cc_final: 0.9294 (tm-30) REVERT: C 250 MET cc_start: 0.9191 (mmm) cc_final: 0.8950 (tpp) REVERT: C 468 MET cc_start: 0.5333 (tmm) cc_final: 0.4800 (tmm) REVERT: D 58 THR cc_start: 0.8760 (p) cc_final: 0.7663 (p) REVERT: F 574 LYS cc_start: 0.9417 (tptp) cc_final: 0.9155 (tptp) REVERT: F 583 ILE cc_start: 0.9745 (OUTLIER) cc_final: 0.9424 (tp) REVERT: F 639 GLU cc_start: 0.9082 (pp20) cc_final: 0.8771 (pp20) REVERT: I 250 MET cc_start: 0.9197 (mmp) cc_final: 0.8837 (tpp) REVERT: I 374 MET cc_start: 0.5712 (pmm) cc_final: 0.5449 (pmm) REVERT: J 107 LEU cc_start: 0.9211 (tp) cc_final: 0.8981 (tp) REVERT: K 30 ASP cc_start: 0.9312 (t70) cc_final: 0.8709 (t0) outliers start: 5 outliers final: 0 residues processed: 141 average time/residue: 0.1379 time to fit residues: 28.6575 Evaluate side-chains 106 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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: 0.4980 chunk 175 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.0170 chunk 60 optimal weight: 0.9980 overall best weight: 2.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 594 ASN ** 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 = 0.3409 r_free = 0.3409 target = 0.046092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.036509 restraints weight = 173200.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.037311 restraints weight = 124280.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.037851 restraints weight = 100263.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.038234 restraints weight = 87196.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.038466 restraints weight = 79343.524| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16083 Z= 0.154 Angle : 0.712 10.616 22047 Z= 0.334 Chirality : 0.047 0.309 2643 Planarity : 0.004 0.035 2619 Dihedral : 4.607 19.963 1971 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.25 % Allowed : 3.45 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.18), residues: 1773 helix: -0.35 (0.28), residues: 291 sheet: -0.22 (0.27), residues: 318 loop : -1.79 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.026 0.001 TYR F 586 PHE 0.016 0.002 PHE F 600 TRP 0.019 0.001 TRP A 610 HIS 0.002 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (15969) covalent geometry : angle 0.67071 / 0.32 (21732) SS BOND : bond 0.00267 / 0.17 ( 27) SS BOND : angle 0.73962 / 0.53 ( 54) hydrogen bonds : bond 0.03861 / 2.41 ( 345) hydrogen bonds : angle 6.23179 / 4.45 ( 927) link_ALPHA1-3 : bond 0.00658 / 0.35 ( 9) link_ALPHA1-3 : angle 1.97101 / 1.32 ( 27) link_ALPHA1-6 : bond 0.00371 / 0.20 ( 6) link_ALPHA1-6 : angle 1.39404 / 0.80 ( 18) link_BETA1-4 : bond 0.00341 / 0.21 ( 30) link_BETA1-4 : angle 1.85458 / 1.30 ( 90) link_NAG-ASN : bond 0.00679 / 0.35 ( 42) link_NAG-ASN : angle 2.72664 / 2.16 ( 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 144 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9546 (tptp) cc_final: 0.9168 (tptp) REVERT: B 583 ILE cc_start: 0.9781 (OUTLIER) cc_final: 0.9464 (tp) REVERT: B 588 LYS cc_start: 0.9766 (tmtt) cc_final: 0.9559 (tptp) REVERT: B 633 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8537 (mtm180) REVERT: B 639 GLU cc_start: 0.9204 (pp20) cc_final: 0.8937 (pp20) REVERT: B 652 GLN cc_start: 0.9713 (tt0) cc_final: 0.9421 (tm-30) REVERT: G 250 MET cc_start: 0.9343 (mmp) cc_final: 0.8773 (tpp) REVERT: G 468 MET cc_start: 0.5569 (tmm) cc_final: 0.4843 (ppp) REVERT: H 60 TYR cc_start: 0.8959 (m-10) cc_final: 0.8603 (m-10) REVERT: H 80 LEU cc_start: 0.9108 (tp) cc_final: 0.8896 (tt) REVERT: A 587 LEU cc_start: 0.9495 (pp) cc_final: 0.9147 (pp) REVERT: A 652 GLN cc_start: 0.9707 (tt0) cc_final: 0.9307 (tm-30) REVERT: C 374 MET cc_start: 0.7464 (pmm) cc_final: 0.7247 (pmm) REVERT: C 468 MET cc_start: 0.5395 (tmm) cc_final: 0.4714 (ppp) REVERT: D 58 THR cc_start: 0.8516 (p) cc_final: 0.7155 (p) REVERT: D 60 TYR cc_start: 0.8850 (m-10) cc_final: 0.8552 (m-10) REVERT: E 70 LYS cc_start: 0.9134 (mmpt) cc_final: 0.8911 (mmmt) REVERT: F 574 LYS cc_start: 0.9470 (tptp) cc_final: 0.9097 (tptp) REVERT: F 583 ILE cc_start: 0.9736 (OUTLIER) cc_final: 0.9369 (tp) REVERT: F 588 LYS cc_start: 0.9761 (tmtt) cc_final: 0.9527 (tptp) REVERT: F 639 GLU cc_start: 0.9131 (pp20) cc_final: 0.8819 (pp20) REVERT: I 250 MET cc_start: 0.9324 (mmp) cc_final: 0.8992 (tpp) REVERT: J 107 LEU cc_start: 0.9194 (tp) cc_final: 0.8974 (tp) REVERT: K 30 ASP cc_start: 0.9376 (t70) cc_final: 0.8728 (t0) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.1181 time to fit residues: 25.3685 Evaluate side-chains 106 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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: 9.9990 chunk 4 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN A 590 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.043678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.034408 restraints weight = 178916.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.035191 restraints weight = 127324.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.035718 restraints weight = 102291.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.036084 restraints weight = 88754.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.036298 restraints weight = 80686.257| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16083 Z= 0.197 Angle : 0.761 9.352 22047 Z= 0.357 Chirality : 0.047 0.321 2643 Planarity : 0.004 0.061 2619 Dihedral : 4.823 20.109 1971 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.19 % Allowed : 2.82 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 1773 helix: -0.21 (0.27), residues: 291 sheet: -0.47 (0.26), residues: 324 loop : -1.86 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 24 TYR 0.031 0.002 TYR F 586 PHE 0.018 0.002 PHE F 600 TRP 0.021 0.002 TRP B 610 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (15969) covalent geometry : angle 0.71818 / 0.35 (21732) SS BOND : bond 0.00357 / 0.25 ( 27) SS BOND : angle 0.73070 / 0.50 ( 54) hydrogen bonds : bond 0.03871 / 2.41 ( 345) hydrogen bonds : angle 6.25305 / 4.46 ( 927) link_ALPHA1-3 : bond 0.00669 / 0.34 ( 9) link_ALPHA1-3 : angle 1.88378 / 1.24 ( 27) link_ALPHA1-6 : bond 0.00233 / 0.11 ( 6) link_ALPHA1-6 : angle 1.44965 / 0.83 ( 18) link_BETA1-4 : bond 0.00425 / 0.25 ( 30) link_BETA1-4 : angle 1.92529 / 1.32 ( 90) link_NAG-ASN : bond 0.00684 / 0.39 ( 42) link_NAG-ASN : angle 2.89462 / 2.27 ( 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 129 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 583 ILE cc_start: 0.9801 (OUTLIER) cc_final: 0.9497 (tp) REVERT: B 588 LYS cc_start: 0.9789 (tmtt) cc_final: 0.9586 (tptp) REVERT: B 639 GLU cc_start: 0.9273 (pp20) cc_final: 0.9013 (pp20) REVERT: B 652 GLN cc_start: 0.9707 (tt0) cc_final: 0.9432 (tm-30) REVERT: G 250 MET cc_start: 0.9282 (mmp) cc_final: 0.8811 (tpp) REVERT: G 468 MET cc_start: 0.6597 (tmm) cc_final: 0.6044 (ppp) REVERT: H 58 THR cc_start: 0.6261 (t) cc_final: 0.5715 (t) REVERT: A 652 GLN cc_start: 0.9696 (tt0) cc_final: 0.9351 (tm-30) REVERT: C 250 MET cc_start: 0.9262 (mmp) cc_final: 0.8699 (tpp) REVERT: C 468 MET cc_start: 0.6128 (tmm) cc_final: 0.5709 (ppp) REVERT: D 58 THR cc_start: 0.8091 (p) cc_final: 0.6590 (p) REVERT: D 60 TYR cc_start: 0.8766 (m-10) cc_final: 0.8561 (m-10) REVERT: E 4 MET cc_start: 0.7397 (mmp) cc_final: 0.7050 (mmm) REVERT: F 574 LYS cc_start: 0.9529 (tptp) cc_final: 0.9166 (tptp) REVERT: F 583 ILE cc_start: 0.9782 (OUTLIER) cc_final: 0.9422 (tp) REVERT: F 588 LYS cc_start: 0.9782 (tmtt) cc_final: 0.9581 (tptp) REVERT: F 639 GLU cc_start: 0.9214 (pp20) cc_final: 0.8939 (pp20) REVERT: J 107 LEU cc_start: 0.9282 (tp) cc_final: 0.9046 (tp) outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.1211 time to fit residues: 23.0630 Evaluate side-chains 97 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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: 8.9990 chunk 156 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 590 GLN H 3 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN D 39 GLN E 37 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.040441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.031621 restraints weight = 191664.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.032419 restraints weight = 130465.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.032976 restraints weight = 102570.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.033301 restraints weight = 87498.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033550 restraints weight = 79338.287| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16083 Z= 0.312 Angle : 0.907 9.578 22047 Z= 0.438 Chirality : 0.052 0.496 2643 Planarity : 0.006 0.070 2619 Dihedral : 5.618 27.563 1971 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.18), residues: 1773 helix: -0.41 (0.26), residues: 303 sheet: -1.33 (0.25), residues: 378 loop : -2.10 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 295 TYR 0.044 0.003 TYR L 32 PHE 0.021 0.003 PHE L 71 TRP 0.024 0.002 TRP G 332 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.31 (15969) covalent geometry : angle 0.86637 / 0.43 (21732) SS BOND : bond 0.00940 / 0.65 ( 27) SS BOND : angle 1.18322 / 0.86 ( 54) hydrogen bonds : bond 0.04455 / 2.77 ( 345) hydrogen bonds : angle 6.75933 / 4.81 ( 927) link_ALPHA1-3 : bond 0.00582 / 0.30 ( 9) link_ALPHA1-3 : angle 1.89307 / 1.27 ( 27) link_ALPHA1-6 : bond 0.00187 / 0.09 ( 6) link_ALPHA1-6 : angle 1.76539 / 1.00 ( 18) link_BETA1-4 : bond 0.00462 / 0.26 ( 30) link_BETA1-4 : angle 2.14692 / 1.45 ( 90) link_NAG-ASN : bond 0.01061 / 0.76 ( 42) link_NAG-ASN : angle 3.05337 / 2.37 ( 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 113 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9583 (tptp) cc_final: 0.9258 (tptt) REVERT: B 639 GLU cc_start: 0.9281 (pp20) cc_final: 0.9061 (pp20) REVERT: B 652 GLN cc_start: 0.9689 (tt0) cc_final: 0.9454 (tm-30) REVERT: G 468 MET cc_start: 0.7170 (tmm) cc_final: 0.6640 (ppp) REVERT: A 652 GLN cc_start: 0.9688 (tt0) cc_final: 0.9420 (tm-30) REVERT: C 374 MET cc_start: 0.8647 (pmm) cc_final: 0.8391 (pmm) REVERT: C 468 MET cc_start: 0.6484 (tmm) cc_final: 0.5929 (ppp) REVERT: D 58 THR cc_start: 0.8031 (p) cc_final: 0.7315 (p) REVERT: D 60 TYR cc_start: 0.8829 (m-10) cc_final: 0.8500 (m-10) REVERT: F 639 GLU cc_start: 0.9315 (pp20) cc_final: 0.9060 (pp20) REVERT: I 468 MET cc_start: 0.6233 (tmm) cc_final: 0.5564 (ppp) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1285 time to fit residues: 21.9206 Evaluate side-chains 81 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 4.9990 chunk 66 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 GLN H 39 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.041863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.032717 restraints weight = 174522.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.033570 restraints weight = 119738.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.034152 restraints weight = 94217.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.034547 restraints weight = 80279.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.034802 restraints weight = 72055.701| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.7259 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= 0.127 Angle : 0.743 12.262 22047 Z= 0.345 Chirality : 0.049 0.299 2643 Planarity : 0.004 0.045 2619 Dihedral : 4.958 20.151 1971 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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 are not related in a simple way. whole: -2.02 (0.19), residues: 1773 helix: -0.13 (0.27), residues: 291 sheet: -1.12 (0.25), residues: 402 loop : -1.84 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 295 TYR 0.016 0.001 TYR L 32 PHE 0.013 0.002 PHE C 236 TRP 0.020 0.001 TRP G 332 HIS 0.002 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (15969) covalent geometry : angle 0.70048 / 0.34 (21732) SS BOND : bond 0.00393 / 0.25 ( 27) SS BOND : angle 0.67590 / 0.49 ( 54) hydrogen bonds : bond 0.03733 / 2.29 ( 345) hydrogen bonds : angle 6.13169 / 4.38 ( 927) link_ALPHA1-3 : bond 0.00681 / 0.36 ( 9) link_ALPHA1-3 : angle 1.91523 / 1.28 ( 27) link_ALPHA1-6 : bond 0.00494 / 0.27 ( 6) link_ALPHA1-6 : angle 1.44991 / 0.83 ( 18) link_BETA1-4 : bond 0.00397 / 0.25 ( 30) link_BETA1-4 : angle 2.00696 / 1.33 ( 90) link_NAG-ASN : bond 0.00605 / 0.36 ( 42) link_NAG-ASN : angle 2.80341 / 2.14 ( 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 121 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9597 (tptp) cc_final: 0.9338 (tptt) REVERT: B 588 LYS cc_start: 0.9825 (tmtt) cc_final: 0.9576 (tptp) REVERT: B 639 GLU cc_start: 0.9327 (pp20) cc_final: 0.9056 (pp20) REVERT: B 652 GLN cc_start: 0.9713 (tt0) cc_final: 0.9443 (tm-30) REVERT: G 468 MET cc_start: 0.7273 (tmm) cc_final: 0.6600 (ppp) REVERT: H 58 THR cc_start: 0.7151 (t) cc_final: 0.6710 (t) REVERT: H 60 TYR cc_start: 0.8779 (m-80) cc_final: 0.8451 (m-10) REVERT: A 584 GLU cc_start: 0.9321 (pp20) cc_final: 0.9105 (pp20) REVERT: A 652 GLN cc_start: 0.9692 (tt0) cc_final: 0.9384 (tm-30) REVERT: C 468 MET cc_start: 0.7001 (tmm) cc_final: 0.6253 (ppp) REVERT: D 58 THR cc_start: 0.7977 (p) cc_final: 0.6326 (p) REVERT: F 574 LYS cc_start: 0.9651 (tptp) cc_final: 0.9308 (tptt) REVERT: F 588 LYS cc_start: 0.9765 (tmtt) cc_final: 0.9533 (tptp) REVERT: F 639 GLU cc_start: 0.9256 (pp20) cc_final: 0.8959 (pp20) REVERT: I 468 MET cc_start: 0.5626 (tmm) cc_final: 0.5083 (ppp) REVERT: J 107 LEU cc_start: 0.9272 (tp) cc_final: 0.9065 (tp) REVERT: K 4 MET cc_start: 0.8641 (mmp) cc_final: 0.8216 (mmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1145 time to fit residues: 21.0303 Evaluate side-chains 95 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 0.9990 chunk 149 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.041964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.032792 restraints weight = 177918.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.033617 restraints weight = 121438.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.034203 restraints weight = 95753.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.034462 restraints weight = 81319.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.034820 restraints weight = 74481.909| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16083 Z= 0.116 Angle : 0.706 11.654 22047 Z= 0.325 Chirality : 0.047 0.308 2643 Planarity : 0.004 0.037 2619 Dihedral : 4.670 19.896 1971 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.06 % Allowed : 0.63 % Favored : 99.31 % 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 are not related in a simple way. whole: -1.78 (0.19), residues: 1773 helix: 0.11 (0.28), residues: 288 sheet: -0.87 (0.26), residues: 417 loop : -1.73 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.012 0.001 TYR B 586 PHE 0.010 0.001 PHE C 236 TRP 0.015 0.001 TRP I 338 HIS 0.001 0.000 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15969) covalent geometry : angle 0.66312 / 0.32 (21732) SS BOND : bond 0.00305 / 0.20 ( 27) SS BOND : angle 0.65719 / 0.48 ( 54) hydrogen bonds : bond 0.03444 / 2.13 ( 345) hydrogen bonds : angle 5.95700 / 4.28 ( 927) link_ALPHA1-3 : bond 0.00671 / 0.36 ( 9) link_ALPHA1-3 : angle 1.89509 / 1.27 ( 27) link_ALPHA1-6 : bond 0.00452 / 0.23 ( 6) link_ALPHA1-6 : angle 1.44127 / 0.83 ( 18) link_BETA1-4 : bond 0.00381 / 0.24 ( 30) link_BETA1-4 : angle 1.93238 / 1.27 ( 90) link_NAG-ASN : bond 0.00598 / 0.36 ( 42) link_NAG-ASN : angle 2.71838 / 2.13 ( 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 118 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9592 (tptp) cc_final: 0.9169 (tptp) REVERT: B 588 LYS cc_start: 0.9826 (tmtt) cc_final: 0.9569 (tptp) REVERT: B 639 GLU cc_start: 0.9283 (pp20) cc_final: 0.8985 (pp20) REVERT: G 250 MET cc_start: 0.9261 (mmm) cc_final: 0.9026 (tpp) REVERT: H 58 THR cc_start: 0.7004 (t) cc_final: 0.6730 (t) REVERT: H 60 TYR cc_start: 0.8734 (m-80) cc_final: 0.8485 (m-10) REVERT: A 584 GLU cc_start: 0.9306 (pp20) cc_final: 0.9070 (pp20) REVERT: A 652 GLN cc_start: 0.9696 (tt0) cc_final: 0.9352 (tm-30) REVERT: C 250 MET cc_start: 0.9320 (mmp) cc_final: 0.8585 (tpp) REVERT: C 468 MET cc_start: 0.6861 (tmm) cc_final: 0.6315 (ppp) REVERT: F 574 LYS cc_start: 0.9621 (tptp) cc_final: 0.9227 (tptt) REVERT: F 588 LYS cc_start: 0.9769 (tmtt) cc_final: 0.9539 (tptp) REVERT: F 639 GLU cc_start: 0.9206 (pp20) cc_final: 0.8945 (pp20) REVERT: I 468 MET cc_start: 0.5345 (tmm) cc_final: 0.4876 (ppp) REVERT: K 4 MET cc_start: 0.8480 (mmp) cc_final: 0.8156 (mmm) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1197 time to fit residues: 21.8256 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 : 0.552 ------------------------------------------------------------------------------- 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: 9.9990 chunk 159 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN C 73 GLN ** C 275 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.040603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.031755 restraints weight = 180044.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032570 restraints weight = 122859.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.033128 restraints weight = 95944.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.033513 restraints weight = 81711.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.033737 restraints weight = 73306.870| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.7754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16083 Z= 0.179 Angle : 0.733 9.468 22047 Z= 0.343 Chirality : 0.046 0.317 2643 Planarity : 0.004 0.049 2619 Dihedral : 4.849 25.290 1971 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.20), residues: 1773 helix: 0.23 (0.28), residues: 291 sheet: -0.81 (0.26), residues: 411 loop : -1.74 (0.19), residues: 1071 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 0.014 0.002 PHE L 62 TRP 0.016 0.001 TRP F 610 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (15969) covalent geometry : angle 0.69277 / 0.33 (21732) SS BOND : bond 0.00309 / 0.21 ( 27) SS BOND : angle 0.77126 / 0.55 ( 54) hydrogen bonds : bond 0.03595 / 2.22 ( 345) hydrogen bonds : angle 6.15650 / 4.41 ( 927) link_ALPHA1-3 : bond 0.00620 / 0.33 ( 9) link_ALPHA1-3 : angle 1.86855 / 1.25 ( 27) link_ALPHA1-6 : bond 0.00240 / 0.10 ( 6) link_ALPHA1-6 : angle 1.50976 / 0.86 ( 18) link_BETA1-4 : bond 0.00342 / 0.21 ( 30) link_BETA1-4 : angle 1.98957 / 1.32 ( 90) link_NAG-ASN : bond 0.00637 / 0.37 ( 42) link_NAG-ASN : angle 2.64824 / 2.11 ( 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 114 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9600 (tptp) cc_final: 0.9327 (tptt) REVERT: B 588 LYS cc_start: 0.9829 (tmtt) cc_final: 0.9606 (tptp) REVERT: B 639 GLU cc_start: 0.9354 (pp20) cc_final: 0.9077 (pp20) REVERT: H 58 THR cc_start: 0.7245 (t) cc_final: 0.6971 (t) REVERT: H 60 TYR cc_start: 0.8761 (m-80) cc_final: 0.8476 (m-10) REVERT: L 70 LYS cc_start: 0.9109 (mmpt) cc_final: 0.8907 (mmmt) REVERT: A 583 ILE cc_start: 0.9781 (mm) cc_final: 0.9580 (tp) REVERT: A 652 GLN cc_start: 0.9701 (tt0) cc_final: 0.9423 (tm-30) REVERT: C 250 MET cc_start: 0.9330 (mmp) cc_final: 0.8779 (tpp) REVERT: D 60 TYR cc_start: 0.8843 (m-10) cc_final: 0.8574 (m-80) REVERT: F 574 LYS cc_start: 0.9652 (tptp) cc_final: 0.9294 (tptt) REVERT: F 588 LYS cc_start: 0.9805 (tmtt) cc_final: 0.9558 (tptp) REVERT: F 639 GLU cc_start: 0.9287 (pp20) cc_final: 0.8991 (pp20) REVERT: I 468 MET cc_start: 0.5802 (tmm) cc_final: 0.5334 (ppp) REVERT: K 4 MET cc_start: 0.8658 (mmp) cc_final: 0.8300 (mmm) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.1211 time to fit residues: 21.1917 Evaluate side-chains 86 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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: 0.0270 chunk 169 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN 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 = 0.3231 r_free = 0.3231 target = 0.039527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.030657 restraints weight = 182523.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.031489 restraints weight = 123361.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.032059 restraints weight = 96042.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.032428 restraints weight = 81326.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.032688 restraints weight = 72870.016| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.8270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16083 Z= 0.183 Angle : 0.749 9.487 22047 Z= 0.350 Chirality : 0.047 0.306 2643 Planarity : 0.004 0.056 2619 Dihedral : 4.989 21.105 1971 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.13 % Allowed : 0.19 % Favored : 99.69 % 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 are not related in a simple way. whole: -1.79 (0.20), residues: 1773 helix: 0.20 (0.28), residues: 291 sheet: -0.91 (0.26), residues: 411 loop : -1.76 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 633 TYR 0.023 0.002 TYR K 32 PHE 0.013 0.002 PHE C 236 TRP 0.023 0.002 TRP C 258 HIS 0.002 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (15969) covalent geometry : angle 0.70857 / 0.34 (21732) SS BOND : bond 0.00462 / 0.25 ( 27) SS BOND : angle 0.77893 / 0.57 ( 54) hydrogen bonds : bond 0.03654 / 2.24 ( 345) hydrogen bonds : angle 6.18822 / 4.42 ( 927) link_ALPHA1-3 : bond 0.00568 / 0.31 ( 9) link_ALPHA1-3 : angle 1.86624 / 1.25 ( 27) link_ALPHA1-6 : bond 0.00241 / 0.11 ( 6) link_ALPHA1-6 : angle 1.53223 / 0.88 ( 18) link_BETA1-4 : bond 0.00349 / 0.22 ( 30) link_BETA1-4 : angle 2.02990 / 1.32 ( 90) link_NAG-ASN : bond 0.00630 / 0.36 ( 42) link_NAG-ASN : angle 2.67693 / 2.13 ( 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 113 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: B 574 LYS cc_start: 0.9591 (tptp) cc_final: 0.9321 (tptt) REVERT: B 588 LYS cc_start: 0.9812 (tmtt) cc_final: 0.9593 (tptp) REVERT: B 639 GLU cc_start: 0.9348 (pp20) cc_final: 0.9066 (pp20) REVERT: H 58 THR cc_start: 0.7483 (t) cc_final: 0.7212 (t) REVERT: H 60 TYR cc_start: 0.8847 (m-80) cc_final: 0.8524 (m-10) REVERT: H 107 LEU cc_start: 0.9355 (tp) cc_final: 0.9155 (tp) REVERT: A 583 ILE cc_start: 0.9764 (mm) cc_final: 0.9544 (tp) REVERT: C 250 MET cc_start: 0.9283 (mmp) cc_final: 0.8646 (tpp) REVERT: E 4 MET cc_start: 0.8479 (mmp) cc_final: 0.8273 (mmm) REVERT: F 574 LYS cc_start: 0.9611 (tptp) cc_final: 0.9244 (tptt) REVERT: F 588 LYS cc_start: 0.9798 (tmtt) cc_final: 0.9558 (tptp) REVERT: F 639 GLU cc_start: 0.9272 (pp20) cc_final: 0.8988 (pp20) REVERT: I 468 MET cc_start: 0.6638 (tmm) cc_final: 0.6045 (ppp) REVERT: J 60 TYR cc_start: 0.9249 (m-80) cc_final: 0.8998 (m-10) REVERT: K 4 MET cc_start: 0.8786 (mmp) cc_final: 0.8397 (mmm) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.1189 time to fit residues: 20.6594 Evaluate side-chains 83 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 135 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 0.0670 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN D 3 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.040507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.031541 restraints weight = 178178.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.032414 restraints weight = 119409.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.033010 restraints weight = 92667.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.033363 restraints weight = 78258.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.033642 restraints weight = 70424.509| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.8218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16083 Z= 0.119 Angle : 0.728 12.444 22047 Z= 0.338 Chirality : 0.048 0.312 2643 Planarity : 0.004 0.048 2619 Dihedral : 4.712 20.563 1971 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.13 % Allowed : 0.19 % Favored : 99.69 % 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 are not related in a simple way. whole: -1.73 (0.20), residues: 1773 helix: 0.18 (0.29), residues: 288 sheet: -0.79 (0.27), residues: 402 loop : -1.72 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.013 0.001 TYR K 32 PHE 0.011 0.001 PHE I 236 TRP 0.020 0.001 TRP I 338 HIS 0.001 0.000 HIS I 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15969) covalent geometry : angle 0.68938 / 0.33 (21732) SS BOND : bond 0.00273 / 0.18 ( 27) SS BOND : angle 0.67659 / 0.49 ( 54) hydrogen bonds : bond 0.03550 / 2.15 ( 345) hydrogen bonds : angle 5.95021 / 4.27 ( 927) link_ALPHA1-3 : bond 0.00621 / 0.33 ( 9) link_ALPHA1-3 : angle 1.88044 / 1.26 ( 27) link_ALPHA1-6 : bond 0.00434 / 0.21 ( 6) link_ALPHA1-6 : angle 1.42330 / 0.82 ( 18) link_BETA1-4 : bond 0.00363 / 0.24 ( 30) link_BETA1-4 : angle 1.97727 / 1.29 ( 90) link_NAG-ASN : bond 0.00593 / 0.35 ( 42) link_NAG-ASN : angle 2.60580 / 2.09 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.97 seconds wall clock time: 40 minutes 15.83 seconds (2415.83 seconds total)