Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 18:03:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb1_40287/05_2023/8sb1_40287_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb1_40287/05_2023/8sb1_40287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb1_40287/05_2023/8sb1_40287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb1_40287/05_2023/8sb1_40287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb1_40287/05_2023/8sb1_40287_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb1_40287/05_2023/8sb1_40287_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.007 sd= 0.213 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 135 5.16 5 C 12465 2.51 5 N 3312 2.21 5 O 4067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "F TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 584": "OE1" <-> "OE2" Residue "G TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 115": "OD1" <-> "OD2" Residue "I TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 664": "OD1" <-> "OD2" Residue "M ASP 73": "OD1" <-> "OD2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 115": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 19979 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.04, per 1000 atoms: 0.50 Number of scatterers: 19979 At special positions: 0 Unit cell: (159.84, 158.76, 136.08, 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 135 16.00 O 4067 8.00 N 3312 7.00 C 12465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.02 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.04 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.02 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.04 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.04 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN S 4 " - " MAN S 5 " " MAN U 4 " - " MAN U 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 10 " " BMA O 3 " - " MAN O 5 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " " BMA W 3 " - " MAN W 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " 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 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-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 2.8 seconds 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 49 sheets defined 19.1% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.819A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.103A pdb=" N ALA A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.666A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.555A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.814A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.507A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.242A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 5.521A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.916A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.603A pdb=" N TYR D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 4.251A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.795A pdb=" N ALA F 60 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR F 61 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 63 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 4.062A pdb=" N ALA F 73 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 115 removed outlier: 3.701A pdb=" N GLN F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.564A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 127' Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.504A pdb=" N PHE F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.956A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 572 through 596 removed outlier: 3.538A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU G 581 " --> pdb=" O GLN G 577 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU G 584 " --> pdb=" O VAL G 580 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU G 593 " --> pdb=" O ASP G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 619 through 624 removed outlier: 4.226A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 637 removed outlier: 5.536A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN G 637 " --> pdb=" O LYS G 633 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 663 removed outlier: 3.927A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU G 663 " --> pdb=" O ASP G 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 27 through 32 removed outlier: 3.651A pdb=" N TYR I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.796A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR K 61 " --> pdb=" O ALA K 58 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS K 63 " --> pdb=" O ALA K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 74 removed outlier: 4.086A pdb=" N ALA K 73 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 115 removed outlier: 3.661A pdb=" N GLN K 103 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 127 removed outlier: 3.590A pdb=" N CYS K 126 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL K 127 " --> pdb=" O PRO K 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 123 through 127' Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 353 Processing helix chain 'K' and resid 387 through 391 Processing helix chain 'K' and resid 475 through 481 removed outlier: 3.847A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 596 removed outlier: 3.548A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU L 581 " --> pdb=" O GLN L 577 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU L 584 " --> pdb=" O VAL L 580 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU L 592 " --> pdb=" O ARG L 588 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU L 593 " --> pdb=" O ASP L 589 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 619 through 624 removed outlier: 3.523A pdb=" N TRP L 623 " --> pdb=" O LEU L 619 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP L 624 " --> pdb=" O SER L 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 619 through 624' Processing helix chain 'L' and resid 627 through 637 removed outlier: 5.471A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE L 635 " --> pdb=" O TRP L 631 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN L 637 " --> pdb=" O LYS L 633 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 663 removed outlier: 3.946A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU L 663 " --> pdb=" O ASP L 659 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 27 through 32 removed outlier: 3.578A pdb=" N TYR N 32 " --> pdb=" O VAL N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 4.284A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.301A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.905A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.977A pdb=" N LYS A 170 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 161 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS A 157 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 176 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.531A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A 434 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 424 " --> pdb=" O MET A 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 215 through 218 removed outlier: 4.499A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.340A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.153A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.196A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.494A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.805A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 383 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.777A pdb=" N VAL A 271 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 11.805A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.494A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.196A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.153A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 309 removed outlier: 3.672A pdb=" N ILE A 309 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.645A pdb=" N THR C 121 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N TYR C 32 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN C 52 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG C 57 " --> pdb=" O ASN C 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 16 through 18 removed outlier: 3.840A pdb=" N ALA C 16 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 18 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER C 84 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.477A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.320A pdb=" N VAL G 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL F 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR G 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TYR F 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N CYS G 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AC2, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.770A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 169 through 176 removed outlier: 3.973A pdb=" N LYS F 170 " --> pdb=" O THR F 161 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 161 " --> pdb=" O LYS F 170 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS F 157 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE F 176 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.565A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET F 434 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE F 424 " --> pdb=" O MET F 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 215 through 218 removed outlier: 4.487A pdb=" N ILE F 215 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY F 250 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR F 217 " --> pdb=" O THR F 248 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 259 through 261 removed outlier: 4.328A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.086A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.371A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.686A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE F 383 " --> pdb=" O PHE F 376 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.787A pdb=" N VAL F 271 " --> pdb=" O HIS F 287 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS F 287 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 11.686A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.371A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.086A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE F 468 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY F 393 " --> pdb=" O TYR F 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 304 through 307 Processing sheet with id=AC9, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.657A pdb=" N THR H 121 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.847A pdb=" N ALA H 16 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL H 18 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER H 84 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.680A pdb=" N VAL I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AD5, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD6, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.383A pdb=" N VAL L 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL K 38 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR L 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR K 40 " --> pdb=" O CYS L 604 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N CYS L 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'K' and resid 55 through 56 Processing sheet with id=AD9, first strand: chain 'K' and resid 91 through 92 removed outlier: 3.989A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 169 through 176 removed outlier: 3.972A pdb=" N LYS K 170 " --> pdb=" O THR K 161 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR K 161 " --> pdb=" O LYS K 170 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS K 157 " --> pdb=" O ALA K 174 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE K 176 " --> pdb=" O LYS K 155 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.624A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET K 434 " --> pdb=" O ILE K 424 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE K 424 " --> pdb=" O MET K 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 215 through 218 removed outlier: 4.567A pdb=" N ILE K 215 " --> pdb=" O GLY K 250 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY K 250 " --> pdb=" O ILE K 215 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR K 217 " --> pdb=" O THR K 248 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.354A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG K 273 " --> pdb=" O ILE K 285 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL K 271 " --> pdb=" O HIS K 287 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.354A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA K 329 " --> pdb=" O CYS K 418 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE K 383 " --> pdb=" O PHE K 376 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE K 376 " --> pdb=" O PHE K 383 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 304 through 309 removed outlier: 3.501A pdb=" N ALA K 319 " --> pdb=" O LYS K 305 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE K 309 " --> pdb=" O GLN K 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 393 through 395 removed outlier: 4.333A pdb=" N GLY K 393 " --> pdb=" O TYR K 361 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N THR K 358 " --> pdb=" O GLU K 466 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE K 468 " --> pdb=" O THR K 358 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.641A pdb=" N THR M 121 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 16 through 18 removed outlier: 3.863A pdb=" N ALA M 16 " --> pdb=" O LEU M 86 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL M 18 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER M 84 " --> pdb=" O VAL M 18 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.619A pdb=" N VAL N 35 " --> pdb=" O TYR N 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR N 51 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AF4, first strand: chain 'N' and resid 18 through 23 611 hydrogen bonds defined for protein. 1557 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: 7.13 Time building geometry restraints manager: 9.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6220 1.34 - 1.46: 5184 1.46 - 1.59: 8809 1.59 - 1.71: 0 1.71 - 1.84: 183 Bond restraints: 20396 Sorted by residual: bond pdb=" C6 BMA E 3 " pdb=" O6 BMA E 3 " ideal model delta sigma weight residual 1.411 1.472 -0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" C6 BMA Q 3 " pdb=" O6 BMA Q 3 " ideal model delta sigma weight residual 1.411 1.471 -0.060 2.00e-02 2.50e+03 8.93e+00 bond pdb=" C6 BMA U 3 " pdb=" O6 BMA U 3 " ideal model delta sigma weight residual 1.411 1.470 -0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" C2 MAN J 5 " pdb=" O2 MAN J 5 " ideal model delta sigma weight residual 1.407 1.463 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" C2 MAN V 5 " pdb=" O2 MAN V 5 " ideal model delta sigma weight residual 1.407 1.462 -0.055 2.00e-02 2.50e+03 7.59e+00 ... (remaining 20391 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.03: 342 105.03 - 112.33: 10586 112.33 - 119.63: 7033 119.63 - 126.93: 9444 126.93 - 134.23: 330 Bond angle restraints: 27735 Sorted by residual: angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 134.23 -12.53 1.80e+00 3.09e-01 4.84e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 134.14 -12.44 1.80e+00 3.09e-01 4.78e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 134.09 -12.39 1.80e+00 3.09e-01 4.74e+01 angle pdb=" C ASN K 403 " pdb=" N SER K 404 " pdb=" CA SER K 404 " ideal model delta sigma weight residual 121.70 131.18 -9.48 1.80e+00 3.09e-01 2.77e+01 angle pdb=" C ASN A 403 " pdb=" N SER A 404 " pdb=" CA SER A 404 " ideal model delta sigma weight residual 121.70 131.00 -9.30 1.80e+00 3.09e-01 2.67e+01 ... (remaining 27730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 10596 17.41 - 34.83: 919 34.83 - 52.24: 156 52.24 - 69.65: 29 69.65 - 87.06: 33 Dihedral angle restraints: 11733 sinusoidal: 4626 harmonic: 7107 Sorted by residual: dihedral pdb=" CB CYS K 119 " pdb=" SG CYS K 119 " pdb=" SG CYS K 205 " pdb=" CB CYS K 205 " ideal model delta sinusoidal sigma weight residual -86.00 -139.82 53.82 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -139.16 53.16 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -138.88 52.88 1 1.00e+01 1.00e-02 3.81e+01 ... (remaining 11730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2625 0.059 - 0.119: 545 0.119 - 0.178: 120 0.178 - 0.238: 16 0.238 - 0.297: 5 Chirality restraints: 3311 Sorted by residual: chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3308 not shown) Planarity restraints: 3453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 123 " 0.051 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO K 124 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO K 124 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO K 124 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.050 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO A 124 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 123 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO F 124 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 124 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 124 " -0.041 5.00e-02 4.00e+02 ... (remaining 3450 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 214 2.61 - 3.18: 18243 3.18 - 3.75: 28114 3.75 - 4.33: 39157 4.33 - 4.90: 64007 Nonbonded interactions: 149735 Sorted by model distance: nonbonded pdb=" OD2 ASP D 84 " pdb=" OH TYR D 88 " model vdw 2.035 2.440 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.080 2.440 nonbonded pdb=" O VAL F 36 " pdb=" OG1 THR G 606 " model vdw 2.083 2.440 nonbonded pdb=" O VAL K 36 " pdb=" OG1 THR L 606 " model vdw 2.113 2.440 nonbonded pdb=" OE1 GLN G 591 " pdb=" OH TYR L 586 " model vdw 2.144 2.440 ... (remaining 149730 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 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'O' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'J' and (resid 2 or resid 5 through 10)) selection = (chain 'R' and (resid 2 or resid 5 through 10)) selection = (chain 'V' and (resid 1 or resid 4 through 9)) } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } ncs_group { reference = chain 'S' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.020 Extract box with map and model: 7.500 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 51.000 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.007 0.061 20396 Z= 0.419 Angle : 0.997 12.529 27735 Z= 0.509 Chirality : 0.054 0.297 3311 Planarity : 0.005 0.075 3441 Dihedral : 13.807 87.064 7065 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.08 % Favored : 92.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -2.33 (0.15), residues: 2442 helix: -0.98 (0.28), residues: 339 sheet: -1.49 (0.19), residues: 594 loop : -1.75 (0.14), residues: 1509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.293 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 outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2844 time to fit residues: 138.7210 Evaluate side-chains 200 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 124 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 0.3980 chunk 141 optimal weight: 8.9990 chunk 220 optimal weight: 30.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN C 1 GLN D 16 GLN G 630 GLN H 1 GLN K 279 ASN K 343 GLN M 1 GLN N 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 20396 Z= 0.217 Angle : 0.679 10.694 27735 Z= 0.351 Chirality : 0.046 0.223 3311 Planarity : 0.004 0.071 3441 Dihedral : 5.957 21.853 2655 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.83 % Favored : 94.80 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -2.18 (0.15), residues: 2442 helix: -0.82 (0.28), residues: 369 sheet: -1.40 (0.19), residues: 606 loop : -1.66 (0.14), residues: 1467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 298 time to evaluate : 2.359 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 outliers start: 4 outliers final: 1 residues processed: 301 average time/residue: 0.2877 time to fit residues: 139.7047 Evaluate side-chains 205 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1769 time to fit residues: 3.3917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 1 GLN F 279 ASN H 1 GLN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN M 1 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.085 20396 Z= 0.424 Angle : 0.801 10.625 27735 Z= 0.413 Chirality : 0.049 0.286 3311 Planarity : 0.005 0.082 3441 Dihedral : 6.222 24.700 2655 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.82 % Favored : 91.81 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -2.41 (0.15), residues: 2442 helix: -1.17 (0.27), residues: 366 sheet: -1.38 (0.18), residues: 663 loop : -1.85 (0.14), residues: 1413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 255 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 256 average time/residue: 0.3039 time to fit residues: 125.9590 Evaluate side-chains 186 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 20396 Z= 0.228 Angle : 0.670 10.897 27735 Z= 0.346 Chirality : 0.045 0.199 3311 Planarity : 0.004 0.074 3441 Dihedral : 5.748 22.739 2655 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.77 % Favored : 93.86 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -2.16 (0.15), residues: 2442 helix: -0.81 (0.28), residues: 360 sheet: -1.17 (0.20), residues: 591 loop : -1.74 (0.14), residues: 1491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.2927 time to fit residues: 124.9537 Evaluate side-chains 185 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.0060 chunk 210 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 20396 Z= 0.181 Angle : 0.642 10.912 27735 Z= 0.329 Chirality : 0.044 0.190 3311 Planarity : 0.004 0.070 3441 Dihedral : 5.411 21.632 2655 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.86 % Favored : 93.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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 (0.16), residues: 2442 helix: -0.53 (0.28), residues: 360 sheet: -0.84 (0.20), residues: 567 loop : -1.60 (0.14), residues: 1515 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2904 time to fit residues: 121.8909 Evaluate side-chains 194 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 19 optimal weight: 0.0570 chunk 77 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 20396 Z= 0.359 Angle : 0.743 10.946 27735 Z= 0.380 Chirality : 0.047 0.236 3311 Planarity : 0.005 0.076 3441 Dihedral : 5.767 28.767 2655 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.03 % Favored : 91.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -1.94 (0.16), residues: 2442 helix: -0.60 (0.28), residues: 348 sheet: -0.83 (0.19), residues: 660 loop : -1.73 (0.15), residues: 1434 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2815 time to fit residues: 113.4557 Evaluate side-chains 187 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 20396 Z= 0.249 Angle : 0.676 11.043 27735 Z= 0.346 Chirality : 0.045 0.217 3311 Planarity : 0.004 0.073 3441 Dihedral : 5.569 27.263 2655 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.22 % Favored : 93.41 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -1.80 (0.16), residues: 2442 helix: -0.20 (0.29), residues: 339 sheet: -0.83 (0.20), residues: 621 loop : -1.64 (0.15), residues: 1482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.2864 time to fit residues: 115.7007 Evaluate side-chains 183 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.0870 chunk 139 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 159 optimal weight: 0.0470 chunk 115 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 20396 Z= 0.178 Angle : 0.647 13.589 27735 Z= 0.329 Chirality : 0.043 0.205 3311 Planarity : 0.004 0.070 3441 Dihedral : 5.187 24.188 2655 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.73 % Favored : 93.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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 (0.16), residues: 2442 helix: -0.27 (0.29), residues: 360 sheet: -0.76 (0.21), residues: 597 loop : -1.53 (0.15), residues: 1485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2858 time to fit residues: 126.1037 Evaluate side-chains 193 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 206 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 20396 Z= 0.369 Angle : 0.734 14.187 27735 Z= 0.375 Chirality : 0.046 0.242 3311 Planarity : 0.005 0.071 3441 Dihedral : 5.567 25.378 2655 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.82 % Favored : 91.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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 (0.16), residues: 2442 helix: -0.34 (0.29), residues: 357 sheet: -0.81 (0.19), residues: 687 loop : -1.67 (0.15), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2835 time to fit residues: 115.3657 Evaluate side-chains 184 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 160 optimal weight: 0.1980 chunk 242 optimal weight: 0.7980 chunk 222 optimal weight: 0.0020 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 20396 Z= 0.184 Angle : 0.666 14.664 27735 Z= 0.338 Chirality : 0.043 0.198 3311 Planarity : 0.004 0.067 3441 Dihedral : 5.237 24.008 2655 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.83 % Favored : 94.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.16), residues: 2442 helix: -0.26 (0.29), residues: 363 sheet: -0.77 (0.20), residues: 618 loop : -1.52 (0.15), residues: 1461 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.036 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 outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2813 time to fit residues: 113.6274 Evaluate side-chains 192 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 GLN ** K 276 ASN ** 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 = 0.3747 r_free = 0.3747 target = 0.124180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113526 restraints weight = 49100.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111903 restraints weight = 99052.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110700 restraints weight = 78370.768| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 20396 Z= 0.274 Angle : 0.689 11.237 27735 Z= 0.352 Chirality : 0.044 0.205 3311 Planarity : 0.004 0.069 3441 Dihedral : 5.363 25.781 2655 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.96 % Favored : 92.67 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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 (0.16), residues: 2442 helix: -0.29 (0.29), residues: 360 sheet: -0.70 (0.19), residues: 687 loop : -1.59 (0.15), residues: 1395 =============================================================================== Job complete usr+sys time: 3208.64 seconds wall clock time: 60 minutes 29.76 seconds (3629.76 seconds total)