Starting phenix.real_space_refine on Tue May 20 14:10:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb1_40287/05_2025/8sb1_40287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb1_40287/05_2025/8sb1_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/cci-nas-00/data/ceres_data/8sb1_40287/05_2025/8sb1_40287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb1_40287/05_2025/8sb1_40287.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb1_40287/05_2025/8sb1_40287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb1_40287/05_2025/8sb1_40287_neut.cif" } resolution = 4.3 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= 0.007 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. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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 dihedrals: 15 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 dihedrals: 30 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 30 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 27 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 dihedrals: 18 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.63, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 6.04 Conformation dependent library (CDL) restraints added in 2.6 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: 2.93 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: 7.43 Time building geometry restraints manager: 6.92 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: 0.00 - 2.51: 26920 2.51 - 5.01: 684 5.01 - 7.52: 105 7.52 - 10.02: 23 10.02 - 12.53: 3 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 - 22.02: 12127 22.02 - 44.04: 711 44.04 - 66.06: 90 66.06 - 88.08: 90 88.08 - 110.10: 36 Dihedral angle restraints: 13054 sinusoidal: 5947 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 13051 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 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.080 3.040 nonbonded pdb=" O VAL F 36 " pdb=" OG1 THR G 606 " model vdw 2.083 3.040 nonbonded pdb=" O VAL K 36 " pdb=" OG1 THR L 606 " model vdw 2.113 3.040 nonbonded pdb=" OE1 GLN G 591 " pdb=" OH TYR L 586 " model vdw 2.144 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 48.260 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.130 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.720 ------------------------------------------------------------------------------- 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 20505 Z= 0.299 Angle : 1.041 12.529 28020 Z= 0.519 Chirality : 0.054 0.297 3311 Planarity : 0.005 0.075 3441 Dihedral : 16.343 110.101 8386 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 % Allowed : 0.28 % Favored : 99.72 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 112 HIS 0.009 0.003 HIS H 35 PHE 0.015 0.002 PHE A 176 TYR 0.020 0.002 TYR K 484 ARG 0.006 0.001 ARG F 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 12) link_NAG-ASN : angle 2.54593 ( 36) link_ALPHA1-6 : bond 0.00697 ( 9) link_ALPHA1-6 : angle 2.43194 ( 27) link_BETA1-4 : bond 0.00624 ( 21) link_BETA1-4 : angle 3.90421 ( 63) link_ALPHA1-2 : bond 0.01038 ( 13) link_ALPHA1-2 : angle 4.29888 ( 39) link_ALPHA1-3 : bond 0.00861 ( 12) link_ALPHA1-3 : angle 3.44558 ( 36) hydrogen bonds : bond 0.24596 ( 583) hydrogen bonds : angle 9.27877 ( 1557) SS BOND : bond 0.00568 ( 42) SS BOND : angle 1.84711 ( 84) covalent geometry : bond 0.00651 (20396) covalent geometry : angle 0.99714 (27735) *********************** 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 to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 2.271 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: A 96 TRP cc_start: 0.8458 (m-90) cc_final: 0.7912 (m-90) REVERT: A 112 TRP cc_start: 0.8461 (t-100) cc_final: 0.7740 (t-100) REVERT: B 584 GLU cc_start: 0.8108 (tp30) cc_final: 0.7811 (tp30) REVERT: C 47 TRP cc_start: 0.8362 (t60) cc_final: 0.8080 (t60) REVERT: C 70 MET cc_start: 0.7254 (ptp) cc_final: 0.6852 (ptt) REVERT: C 90 ASP cc_start: 0.8574 (m-30) cc_final: 0.8198 (m-30) REVERT: D 88 TYR cc_start: 0.4936 (m-10) cc_final: 0.4480 (m-10) REVERT: F 433 CYS cc_start: 0.7185 (t) cc_final: 0.6927 (t) REVERT: H 2 VAL cc_start: 0.6271 (t) cc_final: 0.6038 (t) REVERT: H 70 MET cc_start: 0.7481 (ptm) cc_final: 0.6935 (ptp) REVERT: H 90 ASP cc_start: 0.8432 (m-30) cc_final: 0.8163 (m-30) REVERT: K 96 TRP cc_start: 0.8355 (m-90) cc_final: 0.8066 (m-10) REVERT: K 112 TRP cc_start: 0.8291 (t-100) cc_final: 0.7616 (t-100) REVERT: K 131 CYS cc_start: 0.7509 (t) cc_final: 0.7307 (t) REVERT: M 70 MET cc_start: 0.6818 (ptt) cc_final: 0.6613 (ptt) REVERT: M 114 PHE cc_start: 0.7948 (m-80) cc_final: 0.7647 (m-80) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2791 time to fit residues: 137.1099 Evaluate side-chains 209 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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: 2.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 343 GLN M 1 GLN N 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113727 restraints weight = 48312.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110763 restraints weight = 93942.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109817 restraints weight = 76284.112| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20505 Z= 0.163 Angle : 0.739 12.734 28020 Z= 0.374 Chirality : 0.048 0.260 3311 Planarity : 0.004 0.071 3441 Dihedral : 12.977 86.719 3976 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.95 % Favored : 94.80 % Rotamer: Outliers : 0.14 % Allowed : 4.13 % Favored : 95.73 % 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: -2.14 (0.15), residues: 2442 helix: -0.67 (0.29), residues: 351 sheet: -1.35 (0.20), residues: 564 loop : -1.68 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 96 HIS 0.013 0.001 HIS H 35 PHE 0.011 0.002 PHE H 114 TYR 0.017 0.002 TYR I 48 ARG 0.004 0.000 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 12) link_NAG-ASN : angle 2.43796 ( 36) link_ALPHA1-6 : bond 0.00500 ( 9) link_ALPHA1-6 : angle 2.23995 ( 27) link_BETA1-4 : bond 0.00645 ( 21) link_BETA1-4 : angle 2.12067 ( 63) link_ALPHA1-2 : bond 0.00371 ( 13) link_ALPHA1-2 : angle 2.87493 ( 39) link_ALPHA1-3 : bond 0.01100 ( 12) link_ALPHA1-3 : angle 1.81864 ( 36) hydrogen bonds : bond 0.05276 ( 583) hydrogen bonds : angle 6.91839 ( 1557) SS BOND : bond 0.00310 ( 42) SS BOND : angle 1.01793 ( 84) covalent geometry : bond 0.00368 (20396) covalent geometry : angle 0.71447 (27735) *********************** 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 303 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 300 time to evaluate : 2.221 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: A 40 TYR cc_start: 0.8149 (t80) cc_final: 0.7908 (t80) REVERT: A 112 TRP cc_start: 0.8444 (t-100) cc_final: 0.8024 (t-100) REVERT: B 584 GLU cc_start: 0.8147 (tp30) cc_final: 0.7837 (tp30) REVERT: C 47 TRP cc_start: 0.8197 (t60) cc_final: 0.7926 (t60) REVERT: C 48 MET cc_start: 0.7857 (mmm) cc_final: 0.7538 (mmm) REVERT: C 90 ASP cc_start: 0.8681 (m-30) cc_final: 0.8269 (m-30) REVERT: D 23 THR cc_start: 0.8129 (m) cc_final: 0.7814 (p) REVERT: D 64 PHE cc_start: 0.6550 (m-80) cc_final: 0.6350 (m-10) REVERT: D 72 THR cc_start: 0.7475 (m) cc_final: 0.7223 (p) REVERT: D 88 TYR cc_start: 0.5554 (m-10) cc_final: 0.5295 (m-10) REVERT: F 165 ILE cc_start: 0.8989 (mm) cc_final: 0.8789 (mm) REVERT: G 581 LEU cc_start: 0.8636 (tt) cc_final: 0.8395 (tp) REVERT: H 2 VAL cc_start: 0.6978 (t) cc_final: 0.6746 (t) REVERT: H 90 ASP cc_start: 0.8601 (m-30) cc_final: 0.8175 (m-30) REVERT: I 64 PHE cc_start: 0.6692 (m-80) cc_final: 0.6055 (m-10) REVERT: I 107 LEU cc_start: 0.6864 (tp) cc_final: 0.6630 (tp) REVERT: K 112 TRP cc_start: 0.8358 (t-100) cc_final: 0.7699 (t-100) REVERT: L 584 GLU cc_start: 0.8257 (tp30) cc_final: 0.8028 (tp30) REVERT: M 11 MET cc_start: 0.6975 (mmm) cc_final: 0.6567 (mpp) REVERT: M 47 TRP cc_start: 0.8197 (t60) cc_final: 0.7796 (t60) REVERT: N 23 THR cc_start: 0.8450 (m) cc_final: 0.8236 (p) REVERT: N 64 PHE cc_start: 0.6721 (m-80) cc_final: 0.6058 (m-10) outliers start: 3 outliers final: 1 residues processed: 303 average time/residue: 0.2683 time to fit residues: 131.5358 Evaluate side-chains 209 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 92 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 1 GLN F 279 ASN H 1 GLN K 279 ASN M 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.124291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.111975 restraints weight = 48057.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110010 restraints weight = 102932.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.109032 restraints weight = 74182.080| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20505 Z= 0.169 Angle : 0.732 12.640 28020 Z= 0.370 Chirality : 0.048 0.311 3311 Planarity : 0.004 0.073 3441 Dihedral : 11.896 77.047 3976 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.77 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -0.86 (0.28), residues: 369 sheet: -1.40 (0.19), residues: 630 loop : -1.64 (0.14), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 36 HIS 0.012 0.002 HIS C 35 PHE 0.014 0.002 PHE M 114 TYR 0.020 0.002 TYR F 217 ARG 0.004 0.000 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 12) link_NAG-ASN : angle 2.41878 ( 36) link_ALPHA1-6 : bond 0.00615 ( 9) link_ALPHA1-6 : angle 2.13953 ( 27) link_BETA1-4 : bond 0.00537 ( 21) link_BETA1-4 : angle 1.92274 ( 63) link_ALPHA1-2 : bond 0.00420 ( 13) link_ALPHA1-2 : angle 2.54885 ( 39) link_ALPHA1-3 : bond 0.00973 ( 12) link_ALPHA1-3 : angle 1.65268 ( 36) hydrogen bonds : bond 0.04691 ( 583) hydrogen bonds : angle 6.57384 ( 1557) SS BOND : bond 0.00534 ( 42) SS BOND : angle 1.65773 ( 84) covalent geometry : bond 0.00391 (20396) covalent geometry : angle 0.70724 (27735) *********************** 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 275 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7918 (t80) cc_final: 0.7529 (t80) REVERT: A 96 TRP cc_start: 0.8312 (m-90) cc_final: 0.7940 (m-90) REVERT: A 104 MET cc_start: 0.8468 (tpp) cc_final: 0.8047 (tpp) REVERT: A 434 MET cc_start: 0.9088 (ttp) cc_final: 0.8722 (tmm) REVERT: A 475 MET cc_start: 0.8006 (tpp) cc_final: 0.6914 (tpt) REVERT: A 479 TRP cc_start: 0.8223 (m-90) cc_final: 0.7843 (m-90) REVERT: B 584 GLU cc_start: 0.8188 (tp30) cc_final: 0.7881 (tp30) REVERT: C 48 MET cc_start: 0.7976 (mmm) cc_final: 0.7431 (mmm) REVERT: C 51 ILE cc_start: 0.8699 (mm) cc_final: 0.8476 (mt) REVERT: C 90 ASP cc_start: 0.8618 (m-30) cc_final: 0.8224 (m-30) REVERT: D 23 THR cc_start: 0.7964 (m) cc_final: 0.7645 (p) REVERT: D 72 THR cc_start: 0.7377 (m) cc_final: 0.7113 (p) REVERT: G 636 SER cc_start: 0.6568 (p) cc_final: 0.6053 (m) REVERT: H 90 ASP cc_start: 0.8567 (m-30) cc_final: 0.7901 (m-30) REVERT: I 64 PHE cc_start: 0.6900 (m-80) cc_final: 0.6252 (m-10) REVERT: I 72 THR cc_start: 0.7056 (m) cc_final: 0.6823 (p) REVERT: L 584 GLU cc_start: 0.8202 (tp30) cc_final: 0.7943 (tp30) REVERT: L 627 THR cc_start: 0.6333 (m) cc_final: 0.6106 (m) REVERT: M 47 TRP cc_start: 0.8002 (t60) cc_final: 0.7716 (t60) REVERT: M 48 MET cc_start: 0.8048 (mmm) cc_final: 0.7652 (mmm) REVERT: M 51 ILE cc_start: 0.8945 (mm) cc_final: 0.8726 (mt) REVERT: N 23 THR cc_start: 0.8376 (m) cc_final: 0.8148 (p) REVERT: N 72 THR cc_start: 0.7381 (m) cc_final: 0.6986 (p) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2898 time to fit residues: 126.5838 Evaluate side-chains 202 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 M 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.120877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110989 restraints weight = 48317.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107469 restraints weight = 100265.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106324 restraints weight = 91249.263| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 20505 Z= 0.248 Angle : 0.800 12.546 28020 Z= 0.406 Chirality : 0.049 0.207 3311 Planarity : 0.005 0.078 3441 Dihedral : 11.331 73.284 3976 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.25 % Favored : 92.51 % Rotamer: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.59 % 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: -2.34 (0.15), residues: 2442 helix: -1.11 (0.26), residues: 369 sheet: -1.34 (0.19), residues: 618 loop : -1.80 (0.14), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 36 HIS 0.009 0.002 HIS K 287 PHE 0.016 0.002 PHE A 176 TYR 0.024 0.002 TYR D 93 ARG 0.007 0.001 ARG F 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 12) link_NAG-ASN : angle 2.57344 ( 36) link_ALPHA1-6 : bond 0.00567 ( 9) link_ALPHA1-6 : angle 2.13752 ( 27) link_BETA1-4 : bond 0.00409 ( 21) link_BETA1-4 : angle 1.92046 ( 63) link_ALPHA1-2 : bond 0.00391 ( 13) link_ALPHA1-2 : angle 2.62366 ( 39) link_ALPHA1-3 : bond 0.00798 ( 12) link_ALPHA1-3 : angle 1.56647 ( 36) hydrogen bonds : bond 0.04886 ( 583) hydrogen bonds : angle 6.44500 ( 1557) SS BOND : bond 0.00756 ( 42) SS BOND : angle 1.80602 ( 84) covalent geometry : bond 0.00589 (20396) covalent geometry : angle 0.77588 (27735) *********************** 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 255 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7918 (t80) cc_final: 0.7627 (t80) REVERT: A 95 MET cc_start: 0.7942 (ttp) cc_final: 0.7674 (ttt) REVERT: A 104 MET cc_start: 0.8344 (tpp) cc_final: 0.7924 (tpp) REVERT: A 504 ARG cc_start: 0.7197 (mtt180) cc_final: 0.6920 (mtt180) REVERT: B 584 GLU cc_start: 0.8213 (tp30) cc_final: 0.7921 (tp30) REVERT: C 2 VAL cc_start: 0.6429 (t) cc_final: 0.6187 (t) REVERT: C 90 ASP cc_start: 0.8507 (m-30) cc_final: 0.8113 (m-30) REVERT: D 16 GLN cc_start: 0.5753 (pt0) cc_final: 0.5513 (pt0) REVERT: D 23 THR cc_start: 0.8046 (m) cc_final: 0.7732 (p) REVERT: D 72 THR cc_start: 0.7231 (m) cc_final: 0.6910 (p) REVERT: G 530 MET cc_start: 0.8098 (mmm) cc_final: 0.7890 (mmm) REVERT: H 2 VAL cc_start: 0.6823 (t) cc_final: 0.6567 (t) REVERT: H 11 MET cc_start: 0.7299 (mpp) cc_final: 0.7069 (mpp) REVERT: H 70 MET cc_start: 0.7680 (ptm) cc_final: 0.7407 (ptm) REVERT: H 90 ASP cc_start: 0.8271 (m-30) cc_final: 0.7993 (m-30) REVERT: H 101 TRP cc_start: 0.8356 (t-100) cc_final: 0.8088 (t-100) REVERT: I 64 PHE cc_start: 0.5926 (m-80) cc_final: 0.5376 (m-10) REVERT: I 72 THR cc_start: 0.7006 (m) cc_final: 0.6703 (p) REVERT: K 95 MET cc_start: 0.8164 (ttm) cc_final: 0.7565 (ttm) REVERT: M 47 TRP cc_start: 0.8127 (t60) cc_final: 0.7843 (t60) REVERT: M 48 MET cc_start: 0.8158 (mmm) cc_final: 0.7640 (mmm) REVERT: M 51 ILE cc_start: 0.8948 (mm) cc_final: 0.8683 (mt) REVERT: M 101 TRP cc_start: 0.8549 (t-100) cc_final: 0.8093 (t-100) REVERT: N 23 THR cc_start: 0.8384 (m) cc_final: 0.8168 (p) REVERT: N 72 THR cc_start: 0.7195 (m) cc_final: 0.6740 (p) outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.2721 time to fit residues: 112.7823 Evaluate side-chains 191 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 126 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.125493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116041 restraints weight = 48606.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.112750 restraints weight = 95096.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111703 restraints weight = 85246.476| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20505 Z= 0.173 Angle : 0.719 13.018 28020 Z= 0.364 Chirality : 0.047 0.205 3311 Planarity : 0.005 0.074 3441 Dihedral : 10.447 66.739 3976 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -0.87 (0.27), residues: 369 sheet: -1.26 (0.19), residues: 654 loop : -1.71 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 96 HIS 0.006 0.001 HIS C 35 PHE 0.011 0.002 PHE M 114 TYR 0.022 0.002 TYR N 93 ARG 0.005 0.000 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 12) link_NAG-ASN : angle 2.40159 ( 36) link_ALPHA1-6 : bond 0.00733 ( 9) link_ALPHA1-6 : angle 1.94857 ( 27) link_BETA1-4 : bond 0.00433 ( 21) link_BETA1-4 : angle 1.65639 ( 63) link_ALPHA1-2 : bond 0.00330 ( 13) link_ALPHA1-2 : angle 2.36070 ( 39) link_ALPHA1-3 : bond 0.00961 ( 12) link_ALPHA1-3 : angle 1.43836 ( 36) hydrogen bonds : bond 0.04317 ( 583) hydrogen bonds : angle 6.16192 ( 1557) SS BOND : bond 0.00512 ( 42) SS BOND : angle 1.64766 ( 84) covalent geometry : bond 0.00404 (20396) covalent geometry : angle 0.69713 (27735) *********************** 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 257 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 2.258 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: A 152 GLU cc_start: 0.7300 (tt0) cc_final: 0.6853 (pp20) REVERT: A 377 ASN cc_start: 0.8720 (t0) cc_final: 0.8471 (t0) REVERT: B 584 GLU cc_start: 0.8182 (tp30) cc_final: 0.7930 (tp30) REVERT: H 11 MET cc_start: 0.7345 (mpp) cc_final: 0.7117 (mpp) REVERT: H 90 ASP cc_start: 0.8300 (m-30) cc_final: 0.7969 (m-30) REVERT: H 101 TRP cc_start: 0.8486 (t-100) cc_final: 0.8071 (t-100) REVERT: I 64 PHE cc_start: 0.6067 (m-80) cc_final: 0.5570 (m-10) REVERT: I 72 THR cc_start: 0.6707 (m) cc_final: 0.6485 (p) REVERT: K 359 ILE cc_start: 0.6988 (mt) cc_final: 0.6782 (mt) REVERT: K 377 ASN cc_start: 0.8806 (t0) cc_final: 0.8587 (t0) REVERT: M 48 MET cc_start: 0.7933 (mmm) cc_final: 0.7702 (mmm) REVERT: M 51 ILE cc_start: 0.8787 (mm) cc_final: 0.8559 (mt) REVERT: M 101 TRP cc_start: 0.8566 (t-100) cc_final: 0.8043 (t-100) REVERT: N 72 THR cc_start: 0.7059 (m) cc_final: 0.6627 (p) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2872 time to fit residues: 117.9082 Evaluate side-chains 200 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 13 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** B 543 ASN B 575 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109201 restraints weight = 48039.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109183 restraints weight = 112980.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108902 restraints weight = 68739.609| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20505 Z= 0.176 Angle : 0.723 12.735 28020 Z= 0.364 Chirality : 0.047 0.235 3311 Planarity : 0.005 0.073 3441 Dihedral : 9.780 61.488 3976 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.59 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -2.08 (0.16), residues: 2442 helix: -0.52 (0.28), residues: 351 sheet: -1.23 (0.19), residues: 669 loop : -1.70 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP F 96 HIS 0.007 0.001 HIS C 35 PHE 0.013 0.002 PHE M 114 TYR 0.026 0.002 TYR F 217 ARG 0.005 0.000 ARG M 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 12) link_NAG-ASN : angle 2.30192 ( 36) link_ALPHA1-6 : bond 0.00777 ( 9) link_ALPHA1-6 : angle 1.86471 ( 27) link_BETA1-4 : bond 0.00431 ( 21) link_BETA1-4 : angle 1.59017 ( 63) link_ALPHA1-2 : bond 0.00330 ( 13) link_ALPHA1-2 : angle 2.30701 ( 39) link_ALPHA1-3 : bond 0.00951 ( 12) link_ALPHA1-3 : angle 1.41603 ( 36) hydrogen bonds : bond 0.04256 ( 583) hydrogen bonds : angle 6.08213 ( 1557) SS BOND : bond 0.00610 ( 42) SS BOND : angle 1.71797 ( 84) covalent geometry : bond 0.00413 (20396) covalent geometry : angle 0.70197 (27735) *********************** 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 251 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.7283 (tt0) cc_final: 0.6806 (pp20) REVERT: A 377 ASN cc_start: 0.8815 (t0) cc_final: 0.8524 (t0) REVERT: A 504 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6722 (mtt180) REVERT: B 584 GLU cc_start: 0.8166 (tp30) cc_final: 0.7930 (tp30) REVERT: C 2 VAL cc_start: 0.6406 (t) cc_final: 0.6204 (t) REVERT: C 90 ASP cc_start: 0.8202 (m-30) cc_final: 0.8000 (m-30) REVERT: H 90 ASP cc_start: 0.8407 (m-30) cc_final: 0.8067 (m-30) REVERT: H 101 TRP cc_start: 0.8510 (t-100) cc_final: 0.8058 (t-100) REVERT: I 64 PHE cc_start: 0.6088 (m-80) cc_final: 0.5777 (m-10) REVERT: I 72 THR cc_start: 0.6638 (m) cc_final: 0.6413 (p) REVERT: K 95 MET cc_start: 0.8133 (ttm) cc_final: 0.7580 (ttm) REVERT: K 107 ASP cc_start: 0.7481 (m-30) cc_final: 0.7270 (t0) REVERT: K 359 ILE cc_start: 0.6916 (mt) cc_final: 0.6710 (mt) REVERT: K 377 ASN cc_start: 0.8831 (t0) cc_final: 0.8609 (t0) REVERT: M 11 MET cc_start: 0.7200 (mmm) cc_final: 0.6708 (mpp) REVERT: M 51 ILE cc_start: 0.8968 (mm) cc_final: 0.8742 (mt) REVERT: M 101 TRP cc_start: 0.8619 (t-100) cc_final: 0.8003 (t-100) REVERT: N 72 THR cc_start: 0.6968 (m) cc_final: 0.6654 (p) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2989 time to fit residues: 118.1807 Evaluate side-chains 196 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 92 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 ASN L 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.121728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110515 restraints weight = 47610.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107713 restraints weight = 99620.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106922 restraints weight = 75712.388| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20505 Z= 0.226 Angle : 0.772 12.673 28020 Z= 0.391 Chirality : 0.049 0.221 3311 Planarity : 0.005 0.076 3441 Dihedral : 9.467 59.034 3976 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.21 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -2.08 (0.16), residues: 2442 helix: -0.48 (0.29), residues: 333 sheet: -1.15 (0.18), residues: 768 loop : -1.75 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP F 69 HIS 0.007 0.002 HIS F 287 PHE 0.024 0.002 PHE A 233 TYR 0.023 0.002 TYR N 93 ARG 0.004 0.000 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 12) link_NAG-ASN : angle 2.39887 ( 36) link_ALPHA1-6 : bond 0.00773 ( 9) link_ALPHA1-6 : angle 1.89089 ( 27) link_BETA1-4 : bond 0.00457 ( 21) link_BETA1-4 : angle 1.65197 ( 63) link_ALPHA1-2 : bond 0.00335 ( 13) link_ALPHA1-2 : angle 2.34456 ( 39) link_ALPHA1-3 : bond 0.00930 ( 12) link_ALPHA1-3 : angle 1.45088 ( 36) hydrogen bonds : bond 0.04542 ( 583) hydrogen bonds : angle 6.17903 ( 1557) SS BOND : bond 0.00621 ( 42) SS BOND : angle 1.84472 ( 84) covalent geometry : bond 0.00541 (20396) covalent geometry : angle 0.75128 (27735) *********************** 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 240 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8928 (t0) cc_final: 0.8666 (t0) REVERT: A 504 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6805 (mtt180) REVERT: B 584 GLU cc_start: 0.8195 (tp30) cc_final: 0.7953 (tp30) REVERT: C 51 ILE cc_start: 0.8638 (mt) cc_final: 0.8407 (mt) REVERT: C 90 ASP cc_start: 0.8307 (m-30) cc_final: 0.8064 (m-30) REVERT: D 72 THR cc_start: 0.7142 (m) cc_final: 0.6669 (p) REVERT: F 359 ILE cc_start: 0.7110 (mt) cc_final: 0.6903 (mt) REVERT: H 101 TRP cc_start: 0.8611 (t-100) cc_final: 0.8157 (t-100) REVERT: I 64 PHE cc_start: 0.6140 (m-80) cc_final: 0.5818 (m-10) REVERT: I 72 THR cc_start: 0.6764 (m) cc_final: 0.6478 (p) REVERT: K 359 ILE cc_start: 0.6957 (mt) cc_final: 0.6722 (mt) REVERT: M 82 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7211 (tm-30) REVERT: M 101 TRP cc_start: 0.8688 (t-100) cc_final: 0.8091 (t-100) REVERT: N 72 THR cc_start: 0.7080 (m) cc_final: 0.6726 (p) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2704 time to fit residues: 105.2116 Evaluate side-chains 186 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 49 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 86 optimal weight: 0.0040 chunk 93 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111159 restraints weight = 47710.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.110026 restraints weight = 102589.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108432 restraints weight = 72817.679| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20505 Z= 0.189 Angle : 0.746 12.623 28020 Z= 0.378 Chirality : 0.048 0.221 3311 Planarity : 0.005 0.074 3441 Dihedral : 8.924 59.934 3976 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.84 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -2.04 (0.16), residues: 2442 helix: -0.44 (0.29), residues: 333 sheet: -1.12 (0.18), residues: 771 loop : -1.73 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP A 96 HIS 0.007 0.001 HIS M 35 PHE 0.013 0.002 PHE A 176 TYR 0.021 0.002 TYR D 93 ARG 0.003 0.000 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 2.31092 ( 36) link_ALPHA1-6 : bond 0.00868 ( 9) link_ALPHA1-6 : angle 1.80710 ( 27) link_BETA1-4 : bond 0.00420 ( 21) link_BETA1-4 : angle 1.50508 ( 63) link_ALPHA1-2 : bond 0.00315 ( 13) link_ALPHA1-2 : angle 2.21918 ( 39) link_ALPHA1-3 : bond 0.00975 ( 12) link_ALPHA1-3 : angle 1.37716 ( 36) hydrogen bonds : bond 0.04263 ( 583) hydrogen bonds : angle 6.10876 ( 1557) SS BOND : bond 0.00547 ( 42) SS BOND : angle 1.82739 ( 84) covalent geometry : bond 0.00446 (20396) covalent geometry : angle 0.72675 (27735) *********************** 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 243 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8894 (t0) cc_final: 0.8622 (t0) REVERT: A 434 MET cc_start: 0.9110 (ttp) cc_final: 0.8857 (ttm) REVERT: A 504 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6789 (mtt180) REVERT: B 584 GLU cc_start: 0.8126 (tp30) cc_final: 0.7923 (tp30) REVERT: D 72 THR cc_start: 0.7078 (m) cc_final: 0.6645 (p) REVERT: F 165 ILE cc_start: 0.8851 (mm) cc_final: 0.8612 (mm) REVERT: F 359 ILE cc_start: 0.7076 (mt) cc_final: 0.6848 (mt) REVERT: F 377 ASN cc_start: 0.8847 (t0) cc_final: 0.8609 (t0) REVERT: H 2 VAL cc_start: 0.7134 (t) cc_final: 0.6839 (t) REVERT: H 90 ASP cc_start: 0.8560 (m-30) cc_final: 0.8142 (m-30) REVERT: H 101 TRP cc_start: 0.8617 (t-100) cc_final: 0.8138 (t-100) REVERT: I 64 PHE cc_start: 0.6254 (m-80) cc_final: 0.5863 (m-10) REVERT: I 72 THR cc_start: 0.6686 (m) cc_final: 0.6384 (p) REVERT: K 95 MET cc_start: 0.8359 (ttm) cc_final: 0.7787 (ttm) REVERT: K 359 ILE cc_start: 0.6944 (mt) cc_final: 0.6716 (mt) REVERT: K 377 ASN cc_start: 0.8887 (t0) cc_final: 0.8637 (t0) REVERT: M 2 VAL cc_start: 0.6602 (t) cc_final: 0.6218 (t) REVERT: M 51 ILE cc_start: 0.8832 (mt) cc_final: 0.8613 (mt) REVERT: M 101 TRP cc_start: 0.8727 (t-100) cc_final: 0.8097 (t-100) REVERT: N 72 THR cc_start: 0.6926 (m) cc_final: 0.6602 (p) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2882 time to fit residues: 113.3174 Evaluate side-chains 179 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 0.4980 chunk 174 optimal weight: 8.9990 chunk 205 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112552 restraints weight = 47510.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.110913 restraints weight = 100345.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.109964 restraints weight = 69681.075| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20505 Z= 0.136 Angle : 0.688 12.657 28020 Z= 0.347 Chirality : 0.046 0.211 3311 Planarity : 0.004 0.074 3441 Dihedral : 8.023 58.160 3976 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.10 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -0.19 (0.30), residues: 330 sheet: -0.70 (0.20), residues: 663 loop : -1.59 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 96 HIS 0.004 0.001 HIS M 35 PHE 0.009 0.001 PHE K 176 TYR 0.024 0.001 TYR N 93 ARG 0.002 0.000 ARG K 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 12) link_NAG-ASN : angle 2.13561 ( 36) link_ALPHA1-6 : bond 0.00968 ( 9) link_ALPHA1-6 : angle 1.72717 ( 27) link_BETA1-4 : bond 0.00435 ( 21) link_BETA1-4 : angle 1.30535 ( 63) link_ALPHA1-2 : bond 0.00317 ( 13) link_ALPHA1-2 : angle 2.04555 ( 39) link_ALPHA1-3 : bond 0.01063 ( 12) link_ALPHA1-3 : angle 1.25710 ( 36) hydrogen bonds : bond 0.03786 ( 583) hydrogen bonds : angle 5.88834 ( 1557) SS BOND : bond 0.00436 ( 42) SS BOND : angle 1.55846 ( 84) covalent geometry : bond 0.00309 (20396) covalent geometry : angle 0.67089 (27735) *********************** 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 254 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 2.154 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: A 112 TRP cc_start: 0.8696 (t-100) cc_final: 0.8136 (t-100) REVERT: A 377 ASN cc_start: 0.8855 (t0) cc_final: 0.8636 (t0) REVERT: A 504 ARG cc_start: 0.7086 (mtt180) cc_final: 0.6853 (mtt180) REVERT: C 90 ASP cc_start: 0.8565 (m-30) cc_final: 0.8101 (m-30) REVERT: D 10 VAL cc_start: 0.4925 (p) cc_final: 0.4586 (t) REVERT: D 72 THR cc_start: 0.7072 (m) cc_final: 0.6681 (p) REVERT: F 426 MET cc_start: 0.6731 (ptm) cc_final: 0.6502 (ptm) REVERT: F 433 CYS cc_start: 0.7268 (t) cc_final: 0.7048 (t) REVERT: H 63 LYS cc_start: 0.8387 (pttp) cc_final: 0.8089 (ttpt) REVERT: H 90 ASP cc_start: 0.8481 (m-30) cc_final: 0.8150 (m-30) REVERT: H 101 TRP cc_start: 0.8588 (t-100) cc_final: 0.8076 (t-100) REVERT: I 10 VAL cc_start: 0.5661 (p) cc_final: 0.5298 (t) REVERT: I 16 GLN cc_start: 0.5127 (pt0) cc_final: 0.4898 (pt0) REVERT: I 64 PHE cc_start: 0.6325 (m-80) cc_final: 0.5846 (m-10) REVERT: I 72 THR cc_start: 0.6501 (m) cc_final: 0.6198 (p) REVERT: K 95 MET cc_start: 0.8270 (ttm) cc_final: 0.7679 (ttm) REVERT: K 175 LEU cc_start: 0.8807 (mp) cc_final: 0.8530 (mt) REVERT: K 377 ASN cc_start: 0.8824 (t0) cc_final: 0.8616 (t0) REVERT: L 530 MET cc_start: 0.8096 (mmm) cc_final: 0.7759 (mpp) REVERT: M 82 GLU cc_start: 0.7665 (tp30) cc_final: 0.7324 (tp30) REVERT: M 101 TRP cc_start: 0.8656 (t-100) cc_final: 0.8004 (t-100) REVERT: N 23 THR cc_start: 0.8060 (p) cc_final: 0.7812 (t) REVERT: N 72 THR cc_start: 0.6933 (m) cc_final: 0.6565 (p) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2698 time to fit residues: 111.8204 Evaluate side-chains 191 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 213 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 222 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.125586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112865 restraints weight = 47610.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111035 restraints weight = 102481.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110170 restraints weight = 74047.342| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20505 Z= 0.132 Angle : 0.683 12.629 28020 Z= 0.345 Chirality : 0.046 0.209 3311 Planarity : 0.004 0.073 3441 Dihedral : 7.519 56.102 3976 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.60 (0.16), residues: 2442 helix: -0.26 (0.29), residues: 333 sheet: -0.52 (0.20), residues: 651 loop : -1.55 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 96 HIS 0.004 0.001 HIS F 374 PHE 0.010 0.001 PHE K 53 TYR 0.025 0.001 TYR D 93 ARG 0.007 0.000 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 12) link_NAG-ASN : angle 2.06673 ( 36) link_ALPHA1-6 : bond 0.00942 ( 9) link_ALPHA1-6 : angle 1.68542 ( 27) link_BETA1-4 : bond 0.00438 ( 21) link_BETA1-4 : angle 1.26777 ( 63) link_ALPHA1-2 : bond 0.00334 ( 13) link_ALPHA1-2 : angle 1.96565 ( 39) link_ALPHA1-3 : bond 0.01030 ( 12) link_ALPHA1-3 : angle 1.22925 ( 36) hydrogen bonds : bond 0.03740 ( 583) hydrogen bonds : angle 5.80672 ( 1557) SS BOND : bond 0.00499 ( 42) SS BOND : angle 1.48030 ( 84) covalent geometry : bond 0.00302 (20396) covalent geometry : angle 0.66757 (27735) ********************** 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 260 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 2.124 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: A 95 MET cc_start: 0.7643 (ptm) cc_final: 0.7400 (ppp) REVERT: A 112 TRP cc_start: 0.8567 (t-100) cc_final: 0.8076 (t-100) REVERT: A 377 ASN cc_start: 0.8888 (t0) cc_final: 0.8666 (t0) REVERT: A 504 ARG cc_start: 0.7025 (mtt180) cc_final: 0.6798 (mtt180) REVERT: C 90 ASP cc_start: 0.8505 (m-30) cc_final: 0.8097 (m-30) REVERT: D 10 VAL cc_start: 0.4960 (p) cc_final: 0.4532 (t) REVERT: D 72 THR cc_start: 0.7033 (m) cc_final: 0.6640 (p) REVERT: F 426 MET cc_start: 0.6548 (ptm) cc_final: 0.6256 (ptm) REVERT: G 648 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6968 (pp20) REVERT: H 90 ASP cc_start: 0.8474 (m-30) cc_final: 0.8015 (m-30) REVERT: H 101 TRP cc_start: 0.8525 (t-100) cc_final: 0.8079 (t-100) REVERT: I 10 VAL cc_start: 0.5586 (p) cc_final: 0.5213 (t) REVERT: I 16 GLN cc_start: 0.5086 (pt0) cc_final: 0.4826 (pt0) REVERT: I 64 PHE cc_start: 0.6370 (m-80) cc_final: 0.5853 (m-10) REVERT: K 95 MET cc_start: 0.8196 (ttm) cc_final: 0.7563 (ttm) REVERT: K 175 LEU cc_start: 0.8707 (mp) cc_final: 0.8431 (mt) REVERT: K 359 ILE cc_start: 0.6864 (mt) cc_final: 0.6659 (mt) REVERT: K 377 ASN cc_start: 0.8847 (t0) cc_final: 0.8611 (t0) REVERT: L 530 MET cc_start: 0.8175 (mmm) cc_final: 0.7856 (mpp) REVERT: M 11 MET cc_start: 0.7151 (mmm) cc_final: 0.6587 (mpp) REVERT: M 48 MET cc_start: 0.7735 (mmm) cc_final: 0.7452 (mmm) REVERT: M 81 MET cc_start: 0.8368 (tpp) cc_final: 0.8143 (tpp) REVERT: M 101 TRP cc_start: 0.8650 (t-100) cc_final: 0.8015 (t-100) REVERT: N 23 THR cc_start: 0.7875 (p) cc_final: 0.7652 (t) REVERT: N 72 THR cc_start: 0.6984 (m) cc_final: 0.6638 (p) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2757 time to fit residues: 114.9818 Evaluate side-chains 200 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 543 ASN G 575 GLN G 652 GLN L 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110025 restraints weight = 48357.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107095 restraints weight = 102120.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105957 restraints weight = 77776.744| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20505 Z= 0.256 Angle : 0.802 12.409 28020 Z= 0.408 Chirality : 0.049 0.260 3311 Planarity : 0.005 0.075 3441 Dihedral : 8.279 58.816 3976 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.33 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -2.00 (0.16), residues: 2442 helix: -0.46 (0.29), residues: 330 sheet: -0.92 (0.19), residues: 711 loop : -1.80 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP C 36 HIS 0.007 0.002 HIS F 287 PHE 0.019 0.003 PHE A 176 TYR 0.022 0.002 TYR N 93 ARG 0.005 0.001 ARG K 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 12) link_NAG-ASN : angle 2.40767 ( 36) link_ALPHA1-6 : bond 0.00793 ( 9) link_ALPHA1-6 : angle 1.82344 ( 27) link_BETA1-4 : bond 0.00434 ( 21) link_BETA1-4 : angle 1.52483 ( 63) link_ALPHA1-2 : bond 0.00379 ( 13) link_ALPHA1-2 : angle 2.21186 ( 39) link_ALPHA1-3 : bond 0.00908 ( 12) link_ALPHA1-3 : angle 1.44144 ( 36) hydrogen bonds : bond 0.04584 ( 583) hydrogen bonds : angle 6.13108 ( 1557) SS BOND : bond 0.00743 ( 42) SS BOND : angle 1.81884 ( 84) covalent geometry : bond 0.00610 (20396) covalent geometry : angle 0.78420 (27735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4814.36 seconds wall clock time: 86 minutes 58.12 seconds (5218.12 seconds total)