Starting phenix.real_space_refine on Tue Apr 9 06:30:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dua_27718/04_2024/8dua_27718.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dua_27718/04_2024/8dua_27718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dua_27718/04_2024/8dua_27718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dua_27718/04_2024/8dua_27718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dua_27718/04_2024/8dua_27718.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dua_27718/04_2024/8dua_27718.pdb" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9804 2.51 5 N 2520 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15612 Number of models: 1 Model: "" Number of chains: 33 Chain: "B" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 762 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "G" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2354 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 3 Chain: "H" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 888 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 762 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "C" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2354 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 3 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 888 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "E" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "F" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 762 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "I" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2354 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 3 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 888 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.59, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 7.28 Conformation dependent library (CDL) restraints added in 2.9 seconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 31 sheets defined 22.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'B' and resid 570 through 593 removed outlier: 3.825A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.883A pdb=" N ARG B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 664 removed outlier: 4.374A pdb=" N ALA B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 645 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU B 647 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU B 648 " --> pdb=" O GLN B 644 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS B 662 " --> pdb=" O TYR B 658 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 removed outlier: 4.422A pdb=" N GLN G 73 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.980A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN G 103 " --> pdb=" O THR G 99 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA G 104 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 removed outlier: 3.627A pdb=" N GLU G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU G 347 " --> pdb=" O GLN G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.518A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 removed outlier: 4.153A pdb=" N LEU G 391 " --> pdb=" O MET G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 483 removed outlier: 4.186A pdb=" N TYR G 479 " --> pdb=" O VAL G 475 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 480 " --> pdb=" O ALA G 476 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU G 482 " --> pdb=" O LEU G 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 571 through 593 removed outlier: 3.812A pdb=" N GLN A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.902A pdb=" N ARG A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 664 removed outlier: 4.380A pdb=" N ALA A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 645 " --> pdb=" O ASN A 641 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU A 647 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 648 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 662 " --> pdb=" O TYR A 658 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 4.425A pdb=" N GLN C 73 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.992A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.676A pdb=" N GLU C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.520A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 removed outlier: 4.112A pdb=" N LEU C 391 " --> pdb=" O MET C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.189A pdb=" N TYR C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C 482 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'F' and resid 571 through 593 removed outlier: 3.805A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 620 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.904A pdb=" N ARG F 633 " --> pdb=" O GLN F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 664 removed outlier: 4.375A pdb=" N ALA F 640 " --> pdb=" O ASP F 636 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASN F 641 " --> pdb=" O PHE F 637 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN F 644 " --> pdb=" O ALA F 640 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 645 " --> pdb=" O ASN F 641 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU F 647 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU F 648 " --> pdb=" O GLN F 644 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN F 661 " --> pdb=" O MET F 657 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS F 662 " --> pdb=" O TYR F 658 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU F 663 " --> pdb=" O GLU F 659 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 removed outlier: 4.416A pdb=" N GLN I 73 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 3.993A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN I 103 " --> pdb=" O THR I 99 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA I 104 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 352 removed outlier: 3.642A pdb=" N GLU I 344 " --> pdb=" O GLU I 340 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU I 347 " --> pdb=" O GLN I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.528A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.105A pdb=" N LEU I 391 " --> pdb=" O MET I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 483 removed outlier: 4.184A pdb=" N TYR I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG I 480 " --> pdb=" O ALA I 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU I 482 " --> pdb=" O LEU I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.821A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.513A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 242 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL G 244 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 84 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 272 through 274 removed outlier: 3.787A pdb=" N ILE G 282 " --> pdb=" O TYR G 273 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP G 457 " --> pdb=" O ASN G 465 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN G 465 " --> pdb=" O ASP G 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 293 through 296 removed outlier: 3.568A pdb=" N MET G 294 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.134A pdb=" N GLN H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.648A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.011A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.524A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 44 through 49 removed outlier: 6.017A pdb=" N ARG L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.830A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.511A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 242 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 244 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 84 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 272 through 274 removed outlier: 3.750A pdb=" N ILE C 282 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 281 " --> pdb=" O ALA C 454 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 454 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 293 through 296 removed outlier: 3.585A pdb=" N MET C 294 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 456 through 457 removed outlier: 4.009A pdb=" N ASP C 457 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 465 " --> pdb=" O ASP C 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 5 through 7 removed outlier: 4.125A pdb=" N GLN D 5 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 82 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 20 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.271A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG D 38 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.271A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG D 38 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.911A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.534A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 63 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 49 removed outlier: 6.050A pdb=" N ARG E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN E 37 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.820A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.509A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL I 242 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL I 244 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU I 84 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 272 through 274 removed outlier: 3.716A pdb=" N ILE I 282 " --> pdb=" O TYR I 273 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 293 through 296 removed outlier: 3.597A pdb=" N MET I 294 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 456 through 457 removed outlier: 3.992A pdb=" N ASP I 457 " --> pdb=" O ASN I 465 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN I 465 " --> pdb=" O ASP I 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'J' and resid 5 through 7 removed outlier: 4.127A pdb=" N GLN J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU J 20 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 46 through 47 removed outlier: 4.254A pdb=" N GLU J 46 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 46 through 47 removed outlier: 4.254A pdb=" N GLU J 46 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.998A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.523A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER K 63 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 44 through 49 removed outlier: 6.018A pdb=" N ARG K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN K 37 " --> pdb=" O ARG K 46 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 7.43 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: 100.62 - 107.41: 619 107.41 - 114.21: 9480 114.21 - 121.00: 6490 121.00 - 127.80: 4911 127.80 - 134.59: 232 Bond angle restraints: 21732 Sorted by residual: angle pdb=" CA ASN G 279 " pdb=" CB ASN G 279 " pdb=" CG ASN G 279 " ideal model delta sigma weight residual 112.60 101.82 10.78 1.00e+00 1.00e+00 1.16e+02 angle pdb=" N ASN C 279 " pdb=" CA ASN C 279 " pdb=" C ASN C 279 " ideal model delta sigma weight residual 112.72 103.07 9.65 1.14e+00 7.69e-01 7.16e+01 angle pdb=" N ASN I 279 " pdb=" CA ASN I 279 " pdb=" C ASN I 279 " ideal model delta sigma weight residual 112.23 103.86 8.37 1.26e+00 6.30e-01 4.41e+01 angle pdb=" C ASN I 279 " pdb=" CA ASN I 279 " pdb=" CB ASN I 279 " ideal model delta sigma weight residual 110.38 121.33 -10.95 2.04e+00 2.40e-01 2.88e+01 angle pdb=" N THR C 281 " pdb=" CA THR C 281 " pdb=" C THR C 281 " ideal model delta sigma weight residual 109.14 116.65 -7.51 1.49e+00 4.50e-01 2.54e+01 ... (remaining 21727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 9690 24.04 - 48.07: 592 48.07 - 72.11: 110 72.11 - 96.14: 90 96.14 - 120.18: 63 Dihedral angle restraints: 10545 sinusoidal: 5274 harmonic: 5271 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 147.67 -54.67 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual -86.00 -31.80 -54.20 1 1.00e+01 1.00e-02 3.98e+01 ... (remaining 10542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 2585 0.142 - 0.284: 45 0.284 - 0.426: 12 0.426 - 0.568: 0 0.568 - 0.710: 1 Chirality restraints: 2643 Sorted by residual: chirality pdb=" C1 NAG I1008 " pdb=" ND2 ASN I 279 " pdb=" C2 NAG I1008 " pdb=" O5 NAG I1008 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA GLU C 347 " pdb=" N GLU C 347 " pdb=" C GLU C 347 " pdb=" CB GLU C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA GLU I 347 " pdb=" N GLU I 347 " pdb=" C GLU I 347 " pdb=" CB GLU I 347 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 2640 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I1008 " 0.183 2.00e-02 2.50e+03 1.49e-01 2.79e+02 pdb=" C7 NAG I1008 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG I1008 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG I1008 " -0.239 2.00e-02 2.50e+03 pdb=" O7 NAG I1008 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 277 " -0.025 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C LYS G 277 " 0.088 2.00e-02 2.50e+03 pdb=" O LYS G 277 " -0.034 2.00e-02 2.50e+03 pdb=" N SER G 278 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G1008 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG G1008 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G1008 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G1008 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG G1008 " 0.008 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 115 2.49 - 3.09: 11278 3.09 - 3.70: 20916 3.70 - 4.30: 29338 4.30 - 4.90: 47766 Nonbonded interactions: 109413 Sorted by model distance: nonbonded pdb=" O3 NAG C1003 " pdb=" O7 NAG C1003 " model vdw 1.889 2.440 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.114 2.440 nonbonded pdb=" OD1 ASN A 612 " pdb=" OG1 THR A 614 " model vdw 2.119 2.440 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.131 2.440 nonbonded pdb=" OD1 ASN B 612 " pdb=" OG1 THR B 614 " model vdw 2.133 2.440 ... (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 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: 2.110 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: 7.400 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 42.340 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15969 Z= 0.284 Angle : 0.787 10.952 21732 Z= 0.371 Chirality : 0.058 0.710 2643 Planarity : 0.004 0.149 2619 Dihedral : 19.514 120.178 7074 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.25 % Rotamer: Outliers : 0.19 % Allowed : 0.25 % Favored : 99.56 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1773 helix: -0.84 (0.32), residues: 240 sheet: 0.35 (0.34), residues: 234 loop : -1.54 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 458 HIS 0.009 0.001 HIS C 352 PHE 0.005 0.001 PHE I 53 TYR 0.007 0.001 TYR C 352C ARG 0.002 0.000 ARG C 249 *********************** 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 fitting. rotamer outliers: 3 poor density : 255 time to evaluate : 2.125 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: 0.3651 time to fit residues: 129.8906 Evaluate side-chains 135 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 138 optimal weight: 0.0970 chunk 53 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 160 optimal weight: 0.1980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 661 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN C 377 ASN F 594 ASN F 661 GLN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15969 Z= 0.207 Angle : 0.706 9.263 21732 Z= 0.337 Chirality : 0.051 0.367 2643 Planarity : 0.004 0.046 2619 Dihedral : 16.075 110.330 3738 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 0.31 % Allowed : 2.95 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 1773 helix: -0.13 (0.31), residues: 270 sheet: 0.44 (0.32), residues: 237 loop : -1.67 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 458 HIS 0.002 0.001 HIS G 352 PHE 0.028 0.002 PHE A 600 TYR 0.015 0.001 TYR F 586 ARG 0.011 0.001 ARG D 81 *********************** 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 180 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.907 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: G 468 MET cc_start: 0.1923 (ttp) cc_final: 0.1234 (pmm) REVERT: H 72 ASP cc_start: 0.6647 (p0) cc_final: 0.6368 (p0) REVERT: L 54 LEU cc_start: 0.8218 (tp) cc_final: 0.7701 (tt) REVERT: D 58 THR cc_start: 0.5660 (p) cc_final: 0.4706 (p) REVERT: D 82 ASN cc_start: 0.6005 (p0) cc_final: 0.5751 (p0) REVERT: E 94 ASP cc_start: 0.6838 (t0) cc_final: 0.6574 (t70) REVERT: F 583 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8373 (mm) REVERT: F 645 LEU cc_start: 0.8812 (mm) cc_final: 0.8458 (mm) outliers start: 5 outliers final: 1 residues processed: 177 average time/residue: 0.3076 time to fit residues: 79.5929 Evaluate side-chains 121 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 133 optimal weight: 0.7980 chunk 109 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 143 optimal weight: 0.0030 chunk 159 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 overall best weight: 3.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 15969 Z= 0.321 Angle : 0.760 12.471 21732 Z= 0.369 Chirality : 0.050 0.344 2643 Planarity : 0.004 0.043 2619 Dihedral : 12.224 116.470 3738 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.25 % Allowed : 4.52 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.18), residues: 1773 helix: -0.01 (0.29), residues: 282 sheet: -0.04 (0.27), residues: 288 loop : -1.90 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 36 HIS 0.003 0.001 HIS L 55 PHE 0.017 0.002 PHE L 62 TYR 0.033 0.002 TYR B 586 ARG 0.007 0.001 ARG G 269 *********************** 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 137 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.8594 (tptp) cc_final: 0.8336 (tptt) REVERT: B 583 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8658 (tp) REVERT: G 468 MET cc_start: 0.3730 (tmm) cc_final: 0.3383 (tmm) REVERT: H 72 ASP cc_start: 0.7137 (p0) cc_final: 0.6868 (p0) REVERT: D 20 LEU cc_start: 0.8144 (pt) cc_final: 0.7943 (pt) REVERT: D 58 THR cc_start: 0.6257 (p) cc_final: 0.5045 (p) REVERT: F 587 LEU cc_start: 0.8857 (pp) cc_final: 0.8550 (pp) outliers start: 4 outliers final: 0 residues processed: 133 average time/residue: 0.3171 time to fit residues: 62.7187 Evaluate side-chains 98 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15969 Z= 0.234 Angle : 0.697 9.633 21732 Z= 0.331 Chirality : 0.050 0.341 2643 Planarity : 0.004 0.043 2619 Dihedral : 10.707 109.955 3738 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 0.19 % Allowed : 3.01 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 1773 helix: 0.02 (0.28), residues: 297 sheet: -0.39 (0.27), residues: 318 loop : -1.89 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 610 HIS 0.003 0.001 HIS G 352 PHE 0.024 0.002 PHE F 600 TYR 0.022 0.002 TYR B 586 ARG 0.013 0.001 ARG D 71 *********************** 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 141 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.8531 (tptp) cc_final: 0.8256 (tptt) REVERT: B 583 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8592 (tp) REVERT: G 468 MET cc_start: 0.4742 (tmm) cc_final: 0.4190 (ppp) REVERT: A 587 LEU cc_start: 0.8603 (pp) cc_final: 0.7989 (pp) REVERT: C 468 MET cc_start: 0.3034 (ppp) cc_final: 0.2777 (ppp) REVERT: D 58 THR cc_start: 0.5967 (p) cc_final: 0.4886 (p) REVERT: F 583 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8173 (tp) REVERT: F 587 LEU cc_start: 0.8750 (pp) cc_final: 0.8115 (pp) outliers start: 3 outliers final: 0 residues processed: 138 average time/residue: 0.2982 time to fit residues: 61.2682 Evaluate side-chains 104 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 0.0770 chunk 127 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.0970 chunk 153 optimal weight: 0.4980 chunk 43 optimal weight: 0.4980 overall best weight: 2.0338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 39 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15969 Z= 0.193 Angle : 0.668 9.393 21732 Z= 0.311 Chirality : 0.049 0.351 2643 Planarity : 0.004 0.053 2619 Dihedral : 9.815 110.358 3738 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.18), residues: 1773 helix: 0.25 (0.30), residues: 276 sheet: -0.34 (0.27), residues: 318 loop : -1.85 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 610 HIS 0.002 0.001 HIS G 352 PHE 0.011 0.001 PHE A 600 TYR 0.020 0.001 TYR F 586 ARG 0.005 0.001 ARG C 295 *********************** 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 128 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.8515 (tptp) cc_final: 0.8235 (tptt) REVERT: G 468 MET cc_start: 0.5414 (tmm) cc_final: 0.4987 (ppp) REVERT: C 468 MET cc_start: 0.3256 (ppp) cc_final: 0.3025 (ppp) REVERT: D 58 THR cc_start: 0.5469 (p) cc_final: 0.4389 (p) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2983 time to fit residues: 56.6427 Evaluate side-chains 96 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 6.9990 chunk 154 optimal weight: 0.1980 chunk 33 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 590 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15969 Z= 0.278 Angle : 0.730 9.481 21732 Z= 0.351 Chirality : 0.049 0.336 2643 Planarity : 0.004 0.044 2619 Dihedral : 9.331 107.035 3738 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.01 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.19), residues: 1773 helix: 0.21 (0.28), residues: 309 sheet: -0.77 (0.25), residues: 387 loop : -2.05 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 610 HIS 0.003 0.001 HIS L 55 PHE 0.022 0.002 PHE L 62 TYR 0.038 0.002 TYR L 32 ARG 0.004 0.001 ARG E 46 *********************** 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 119 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.8588 (tptp) cc_final: 0.8351 (tptt) REVERT: G 468 MET cc_start: 0.5533 (tmm) cc_final: 0.4919 (ppp) REVERT: C 468 MET cc_start: 0.4356 (ppp) cc_final: 0.4151 (ppp) REVERT: D 58 THR cc_start: 0.5952 (p) cc_final: 0.5314 (p) REVERT: I 374 MET cc_start: 0.5533 (pmm) cc_final: 0.5260 (pmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2849 time to fit residues: 51.2490 Evaluate side-chains 86 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15969 Z= 0.300 Angle : 0.758 9.471 21732 Z= 0.363 Chirality : 0.051 0.409 2643 Planarity : 0.005 0.047 2619 Dihedral : 9.184 102.449 3738 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.28 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.19), residues: 1773 helix: 0.01 (0.28), residues: 309 sheet: -1.12 (0.25), residues: 396 loop : -2.05 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 332 HIS 0.004 0.001 HIS C 275 PHE 0.027 0.002 PHE A 600 TYR 0.035 0.002 TYR B 586 ARG 0.016 0.001 ARG K 24 *********************** 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 106 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.8597 (tptp) cc_final: 0.8388 (tptt) REVERT: G 468 MET cc_start: 0.6421 (tmm) cc_final: 0.5952 (ppp) REVERT: H 80 LEU cc_start: 0.8005 (tp) cc_final: 0.7682 (tt) REVERT: C 468 MET cc_start: 0.5171 (ppp) cc_final: 0.4806 (ppp) REVERT: I 468 MET cc_start: 0.4387 (tmm) cc_final: 0.4159 (tmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2907 time to fit residues: 46.6341 Evaluate side-chains 79 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15969 Z= 0.165 Angle : 0.672 12.006 21732 Z= 0.316 Chirality : 0.049 0.344 2643 Planarity : 0.004 0.031 2619 Dihedral : 8.842 100.352 3738 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.19), residues: 1773 helix: -0.19 (0.28), residues: 315 sheet: -0.99 (0.25), residues: 420 loop : -1.79 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 332 HIS 0.003 0.001 HIS G 352 PHE 0.010 0.001 PHE A 600 TYR 0.017 0.001 TYR B 586 ARG 0.007 0.001 ARG B 579 *********************** 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 116 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 468 MET cc_start: 0.6332 (tmm) cc_final: 0.5554 (ppp) REVERT: C 468 MET cc_start: 0.4870 (ppp) cc_final: 0.4584 (ppp) REVERT: D 58 THR cc_start: 0.5157 (p) cc_final: 0.4552 (p) REVERT: D 75 LYS cc_start: 0.8878 (pptt) cc_final: 0.8418 (tppt) REVERT: I 468 MET cc_start: 0.4116 (tmm) cc_final: 0.3730 (ppp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2812 time to fit residues: 49.7342 Evaluate side-chains 81 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 143 optimal weight: 0.0070 chunk 150 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15969 Z= 0.172 Angle : 0.659 10.711 21732 Z= 0.310 Chirality : 0.048 0.360 2643 Planarity : 0.004 0.033 2619 Dihedral : 8.675 97.651 3738 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1773 helix: -0.18 (0.28), residues: 315 sheet: -0.79 (0.25), residues: 414 loop : -1.80 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 610 HIS 0.002 0.000 HIS G 352 PHE 0.011 0.001 PHE B 600 TYR 0.017 0.001 TYR B 586 ARG 0.003 0.000 ARG J 81 *********************** 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 107 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 58 THR cc_start: 0.6094 (p) cc_final: 0.5340 (p) REVERT: D 75 LYS cc_start: 0.8799 (pptt) cc_final: 0.8325 (tppt) REVERT: I 468 MET cc_start: 0.4227 (tmm) cc_final: 0.3824 (ppp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2732 time to fit residues: 45.4527 Evaluate side-chains 79 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 0.0770 chunk 86 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.7965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15969 Z= 0.215 Angle : 0.682 9.556 21732 Z= 0.326 Chirality : 0.048 0.349 2643 Planarity : 0.004 0.033 2619 Dihedral : 8.524 90.450 3738 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1773 helix: -0.08 (0.28), residues: 315 sheet: -0.98 (0.25), residues: 423 loop : -1.71 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 33 HIS 0.002 0.001 HIS C 275 PHE 0.010 0.002 PHE L 62 TYR 0.020 0.001 TYR A 586 ARG 0.005 0.001 ARG H 94 ********************** 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 105 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 58 THR cc_start: 0.6162 (p) cc_final: 0.5864 (p) REVERT: F 574 LYS cc_start: 0.8345 (tptp) cc_final: 0.8088 (tptt) REVERT: J 60 TYR cc_start: 0.6649 (m-80) cc_final: 0.6438 (m-80) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2681 time to fit residues: 43.4040 Evaluate side-chains 78 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.0010 chunk 129 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 144 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.041831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.032853 restraints weight = 175411.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.033720 restraints weight = 119584.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.034312 restraints weight = 93267.732| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.7941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15969 Z= 0.151 Angle : 0.657 13.467 21732 Z= 0.307 Chirality : 0.048 0.349 2643 Planarity : 0.004 0.033 2619 Dihedral : 8.383 86.929 3738 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1773 helix: -0.07 (0.28), residues: 315 sheet: -0.80 (0.26), residues: 423 loop : -1.64 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 338 HIS 0.002 0.001 HIS G 352 PHE 0.010 0.001 PHE A 600 TYR 0.016 0.001 TYR A 586 ARG 0.003 0.000 ARG G 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.63 seconds wall clock time: 50 minutes 19.55 seconds (3019.55 seconds total)