Starting phenix.real_space_refine on Sun Aug 24 13:10:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb1_40287/08_2025/8sb1_40287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb1_40287/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sb1_40287/08_2025/8sb1_40287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb1_40287/08_2025/8sb1_40287_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sb1_40287/08_2025/8sb1_40287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb1_40287/08_2025/8sb1_40287.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.57, per 1000 atoms: 0.23 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: 1.91 Conformation dependent library (CDL) restraints added in 671.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.69 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: 3.35 Time building geometry restraints manager: 2.45 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: 2.250 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.530 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- 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 : 3.11 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (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 ARG 0.006 0.001 ARG F 298 TYR 0.020 0.002 TYR K 484 PHE 0.015 0.002 PHE A 176 TRP 0.022 0.002 TRP K 112 HIS 0.009 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00651 (20396) covalent geometry : angle 0.99714 (27735) SS BOND : bond 0.00568 ( 42) SS BOND : angle 1.84711 ( 84) hydrogen bonds : bond 0.24596 ( 583) hydrogen bonds : angle 9.27877 ( 1557) 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) 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_NAG-ASN : bond 0.00588 ( 12) link_NAG-ASN : angle 2.54593 ( 36) *********************** 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 : 0.769 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 96 TRP cc_start: 0.8458 (m-90) cc_final: 0.7909 (m-90) REVERT: A 112 TRP cc_start: 0.8461 (t-100) cc_final: 0.7743 (t-100) REVERT: B 584 GLU cc_start: 0.8108 (tp30) cc_final: 0.7808 (tp30) REVERT: C 47 TRP cc_start: 0.8362 (t60) cc_final: 0.8085 (t60) REVERT: C 70 MET cc_start: 0.7254 (ptp) cc_final: 0.6860 (ptt) REVERT: C 90 ASP cc_start: 0.8574 (m-30) cc_final: 0.8008 (m-30) REVERT: D 88 TYR cc_start: 0.4936 (m-10) cc_final: 0.4481 (m-10) REVERT: F 104 MET cc_start: 0.8480 (ttm) cc_final: 0.8251 (ttm) 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: 0.6045 (t) REVERT: H 70 MET cc_start: 0.7481 (ptm) cc_final: 0.6934 (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: 0.8057 (m-10) REVERT: K 112 TRP cc_start: 0.8291 (t-100) cc_final: 0.7675 (t-100) REVERT: M 2 VAL cc_start: 0.6450 (t) cc_final: 0.6183 (t) REVERT: M 70 MET cc_start: 0.6818 (ptt) cc_final: 0.6593 (ptt) REVERT: M 114 PHE cc_start: 0.7948 (m-80) cc_final: 0.7550 (m-80) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1122 time to fit residues: 55.6607 Evaluate side-chains 206 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.123637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.112837 restraints weight = 46756.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109999 restraints weight = 89887.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108905 restraints weight = 70509.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108630 restraints weight = 88689.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108507 restraints weight = 63340.130| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20505 Z= 0.178 Angle : 0.750 13.057 28020 Z= 0.379 Chirality : 0.048 0.227 3311 Planarity : 0.005 0.072 3441 Dihedral : 12.869 84.986 3976 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.68 % Rotamer: Outliers : 0.19 % Allowed : 4.45 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.15), residues: 2442 helix: -0.87 (0.28), residues: 369 sheet: -1.37 (0.20), residues: 579 loop : -1.76 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.018 0.002 TYR I 48 PHE 0.013 0.002 PHE H 114 TRP 0.032 0.002 TRP F 96 HIS 0.013 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00403 (20396) covalent geometry : angle 0.72457 (27735) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.07345 ( 84) hydrogen bonds : bond 0.05196 ( 583) hydrogen bonds : angle 6.85469 ( 1557) link_ALPHA1-2 : bond 0.00297 ( 13) link_ALPHA1-2 : angle 2.75698 ( 39) link_ALPHA1-3 : bond 0.01045 ( 12) link_ALPHA1-3 : angle 1.85908 ( 36) link_ALPHA1-6 : bond 0.00521 ( 9) link_ALPHA1-6 : angle 2.32082 ( 27) link_BETA1-4 : bond 0.00551 ( 21) link_BETA1-4 : angle 2.22537 ( 63) link_NAG-ASN : bond 0.00635 ( 12) link_NAG-ASN : angle 2.45086 ( 36) *********************** 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 300 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 296 time to evaluate : 0.756 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 40 TYR cc_start: 0.8162 (t80) cc_final: 0.7896 (t80) REVERT: A 96 TRP cc_start: 0.8482 (m-90) cc_final: 0.7989 (m-90) REVERT: A 112 TRP cc_start: 0.8450 (t-100) cc_final: 0.8135 (t-100) REVERT: B 584 GLU cc_start: 0.8250 (tp30) cc_final: 0.7953 (tp30) REVERT: C 47 TRP cc_start: 0.8280 (t60) cc_final: 0.7948 (t60) REVERT: C 48 MET cc_start: 0.7869 (mmm) cc_final: 0.7545 (mmm) REVERT: C 90 ASP cc_start: 0.8724 (m-30) cc_final: 0.8238 (m-30) REVERT: D 23 THR cc_start: 0.8169 (m) cc_final: 0.7856 (p) REVERT: D 64 PHE cc_start: 0.6616 (m-80) cc_final: 0.6282 (m-10) REVERT: D 72 THR cc_start: 0.7471 (m) cc_final: 0.7238 (p) REVERT: D 88 TYR cc_start: 0.5661 (m-10) cc_final: 0.5398 (m-10) REVERT: F 165 ILE cc_start: 0.9055 (mm) cc_final: 0.8836 (mm) REVERT: G 581 LEU cc_start: 0.8633 (tt) cc_final: 0.8389 (tp) REVERT: H 90 ASP cc_start: 0.8611 (m-30) cc_final: 0.8209 (m-30) REVERT: I 64 PHE cc_start: 0.6810 (m-80) cc_final: 0.6218 (m-10) REVERT: I 93 TYR cc_start: 0.8438 (t80) cc_final: 0.8169 (t80) REVERT: I 107 LEU cc_start: 0.6922 (tp) cc_final: 0.6660 (tp) REVERT: K 95 MET cc_start: 0.8078 (ttm) cc_final: 0.7860 (ttm) REVERT: K 112 TRP cc_start: 0.8393 (t-100) cc_final: 0.7712 (t-100) REVERT: L 584 GLU cc_start: 0.8311 (tp30) cc_final: 0.8095 (tp30) REVERT: M 11 MET cc_start: 0.7032 (mmm) cc_final: 0.6663 (mpp) REVERT: M 47 TRP cc_start: 0.8247 (t60) cc_final: 0.7826 (t60) REVERT: M 48 MET cc_start: 0.8073 (mmm) cc_final: 0.7863 (mmm) REVERT: M 51 ILE cc_start: 0.9020 (mm) cc_final: 0.8760 (mt) REVERT: N 23 THR cc_start: 0.8477 (m) cc_final: 0.8260 (p) REVERT: N 64 PHE cc_start: 0.6741 (m-80) cc_final: 0.6045 (m-10) outliers start: 4 outliers final: 2 residues processed: 300 average time/residue: 0.1115 time to fit residues: 54.7613 Evaluate side-chains 209 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 154 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.123726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.111550 restraints weight = 48621.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109733 restraints weight = 96666.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108192 restraints weight = 71782.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107774 restraints weight = 89012.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107907 restraints weight = 58602.903| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20505 Z= 0.177 Angle : 0.745 12.619 28020 Z= 0.376 Chirality : 0.048 0.309 3311 Planarity : 0.005 0.074 3441 Dihedral : 11.754 75.716 3976 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.10 % Favored : 93.65 % Rotamer: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.15), residues: 2442 helix: -1.02 (0.27), residues: 369 sheet: -1.41 (0.19), residues: 630 loop : -1.68 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 298 TYR 0.025 0.002 TYR F 217 PHE 0.022 0.002 PHE M 114 TRP 0.042 0.002 TRP C 36 HIS 0.009 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00408 (20396) covalent geometry : angle 0.71782 (27735) SS BOND : bond 0.00476 ( 42) SS BOND : angle 2.03570 ( 84) hydrogen bonds : bond 0.04755 ( 583) hydrogen bonds : angle 6.57307 ( 1557) link_ALPHA1-2 : bond 0.00387 ( 13) link_ALPHA1-2 : angle 2.57631 ( 39) link_ALPHA1-3 : bond 0.00904 ( 12) link_ALPHA1-3 : angle 1.61608 ( 36) link_ALPHA1-6 : bond 0.00593 ( 9) link_ALPHA1-6 : angle 2.12762 ( 27) link_BETA1-4 : bond 0.00500 ( 21) link_BETA1-4 : angle 1.85174 ( 63) link_NAG-ASN : bond 0.00442 ( 12) link_NAG-ASN : angle 2.48489 ( 36) *********************** 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 278 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.815 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: A 40 TYR cc_start: 0.8015 (t80) cc_final: 0.7574 (t80) REVERT: A 96 TRP cc_start: 0.8503 (m-90) cc_final: 0.7998 (m-90) REVERT: A 104 MET cc_start: 0.8504 (tpp) cc_final: 0.8190 (tpp) REVERT: A 434 MET cc_start: 0.9065 (ttp) cc_final: 0.8730 (tmm) REVERT: B 584 GLU cc_start: 0.8209 (tp30) cc_final: 0.7945 (tp30) REVERT: C 2 VAL cc_start: 0.6149 (t) cc_final: 0.5910 (t) REVERT: C 48 MET cc_start: 0.8062 (mmm) cc_final: 0.7437 (mmm) REVERT: C 90 ASP cc_start: 0.8688 (m-30) cc_final: 0.8237 (m-30) REVERT: D 23 THR cc_start: 0.8017 (m) cc_final: 0.7686 (p) REVERT: D 72 THR cc_start: 0.7411 (m) cc_final: 0.7181 (p) REVERT: H 90 ASP cc_start: 0.8557 (m-30) cc_final: 0.7919 (m-30) REVERT: I 64 PHE cc_start: 0.6880 (m-80) cc_final: 0.6233 (m-10) REVERT: I 72 THR cc_start: 0.7069 (m) cc_final: 0.6840 (p) REVERT: L 584 GLU cc_start: 0.8259 (tp30) cc_final: 0.8011 (tp30) REVERT: L 627 THR cc_start: 0.6420 (m) cc_final: 0.6185 (m) REVERT: M 2 VAL cc_start: 0.6626 (t) cc_final: 0.6425 (t) REVERT: M 11 MET cc_start: 0.7664 (mmt) cc_final: 0.7381 (mmm) REVERT: M 47 TRP cc_start: 0.8073 (t60) cc_final: 0.7584 (t60) REVERT: M 48 MET cc_start: 0.8118 (mmm) cc_final: 0.7565 (mmm) REVERT: N 23 THR cc_start: 0.8397 (m) cc_final: 0.8175 (p) REVERT: N 68 LYS cc_start: 0.7651 (tttp) cc_final: 0.7369 (tttm) REVERT: N 72 THR cc_start: 0.7420 (m) cc_final: 0.7033 (p) outliers start: 2 outliers final: 0 residues processed: 276 average time/residue: 0.1341 time to fit residues: 58.8018 Evaluate side-chains 198 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 170 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 149 optimal weight: 0.0770 chunk 168 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.125971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113677 restraints weight = 48131.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111627 restraints weight = 98884.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.110673 restraints weight = 71673.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110463 restraints weight = 84055.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110455 restraints weight = 65194.565| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20505 Z= 0.132 Angle : 0.687 12.652 28020 Z= 0.346 Chirality : 0.046 0.218 3311 Planarity : 0.004 0.068 3441 Dihedral : 10.475 68.084 3976 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.20 % Favored : 94.55 % Rotamer: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.16), residues: 2442 helix: -0.76 (0.28), residues: 369 sheet: -0.93 (0.20), residues: 570 loop : -1.56 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.024 0.001 TYR D 93 PHE 0.013 0.001 PHE M 64 TRP 0.041 0.002 TRP F 96 HIS 0.005 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00294 (20396) covalent geometry : angle 0.66463 (27735) SS BOND : bond 0.00521 ( 42) SS BOND : angle 1.61750 ( 84) hydrogen bonds : bond 0.04042 ( 583) hydrogen bonds : angle 6.07282 ( 1557) link_ALPHA1-2 : bond 0.00352 ( 13) link_ALPHA1-2 : angle 2.31728 ( 39) link_ALPHA1-3 : bond 0.01068 ( 12) link_ALPHA1-3 : angle 1.47323 ( 36) link_ALPHA1-6 : bond 0.00774 ( 9) link_ALPHA1-6 : angle 1.89762 ( 27) link_BETA1-4 : bond 0.00488 ( 21) link_BETA1-4 : angle 1.65339 ( 63) link_NAG-ASN : bond 0.00438 ( 12) link_NAG-ASN : angle 2.28713 ( 36) *********************** 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 268 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.676 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 40 TYR cc_start: 0.7901 (t80) cc_final: 0.7550 (t80) REVERT: A 96 TRP cc_start: 0.8498 (m-90) cc_final: 0.8000 (m-90) REVERT: A 377 ASN cc_start: 0.8695 (t0) cc_final: 0.8493 (t0) REVERT: A 426 MET cc_start: 0.6314 (ptm) cc_final: 0.6056 (ptp) REVERT: A 475 MET cc_start: 0.7427 (tpt) cc_final: 0.7186 (tpt) REVERT: B 584 GLU cc_start: 0.8269 (tp30) cc_final: 0.7988 (tp30) REVERT: B 636 SER cc_start: 0.6251 (p) cc_final: 0.5833 (m) REVERT: C 90 ASP cc_start: 0.8605 (m-30) cc_final: 0.8055 (m-30) REVERT: D 23 THR cc_start: 0.8070 (m) cc_final: 0.7805 (p) REVERT: F 433 CYS cc_start: 0.7249 (t) cc_final: 0.7019 (t) REVERT: G 636 SER cc_start: 0.6296 (p) cc_final: 0.5798 (m) REVERT: H 2 VAL cc_start: 0.7043 (t) cc_final: 0.6819 (t) REVERT: H 90 ASP cc_start: 0.8217 (m-30) cc_final: 0.7803 (m-30) REVERT: H 101 TRP cc_start: 0.8232 (t-100) cc_final: 0.7984 (t-100) REVERT: I 64 PHE cc_start: 0.5944 (m-80) cc_final: 0.5453 (m-10) REVERT: I 72 THR cc_start: 0.6949 (m) cc_final: 0.6741 (p) REVERT: K 95 MET cc_start: 0.8163 (ttm) cc_final: 0.7763 (ttm) REVERT: K 377 ASN cc_start: 0.8627 (t0) cc_final: 0.8420 (t0) REVERT: K 433 CYS cc_start: 0.7492 (t) cc_final: 0.7176 (t) REVERT: L 636 SER cc_start: 0.6883 (p) cc_final: 0.6358 (m) REVERT: M 11 MET cc_start: 0.7705 (mmt) cc_final: 0.7248 (mmm) REVERT: M 47 TRP cc_start: 0.7909 (t60) cc_final: 0.7482 (t60) REVERT: M 48 MET cc_start: 0.7987 (mmm) cc_final: 0.7560 (mmm) REVERT: M 101 TRP cc_start: 0.8303 (t-100) cc_final: 0.8015 (t-100) REVERT: N 23 THR cc_start: 0.8345 (m) cc_final: 0.8109 (p) REVERT: N 68 LYS cc_start: 0.7640 (tttp) cc_final: 0.7435 (tttt) REVERT: N 72 THR cc_start: 0.7217 (m) cc_final: 0.6929 (p) outliers start: 1 outliers final: 1 residues processed: 268 average time/residue: 0.1207 time to fit residues: 52.9977 Evaluate side-chains 206 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 42 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 85 optimal weight: 0.0060 overall best weight: 5.2004 ------------------------------------------------------------------------------- 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** A 279 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.121567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.111850 restraints weight = 48589.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107750 restraints weight = 101595.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106748 restraints weight = 94936.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106821 restraints weight = 84137.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107165 restraints weight = 55353.353| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 20505 Z= 0.336 Angle : 0.897 12.469 28020 Z= 0.452 Chirality : 0.052 0.207 3311 Planarity : 0.006 0.081 3441 Dihedral : 11.015 70.268 3976 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.15), residues: 2442 helix: -1.25 (0.26), residues: 369 sheet: -1.32 (0.18), residues: 693 loop : -1.89 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 298 TYR 0.028 0.003 TYR A 191 PHE 0.022 0.003 PHE A 159 TRP 0.062 0.003 TRP K 96 HIS 0.012 0.003 HIS F 287 Details of bonding type rmsd covalent geometry : bond 0.00803 (20396) covalent geometry : angle 0.87322 (27735) SS BOND : bond 0.00745 ( 42) SS BOND : angle 2.09373 ( 84) hydrogen bonds : bond 0.05335 ( 583) hydrogen bonds : angle 6.53726 ( 1557) link_ALPHA1-2 : bond 0.00429 ( 13) link_ALPHA1-2 : angle 2.65021 ( 39) link_ALPHA1-3 : bond 0.00828 ( 12) link_ALPHA1-3 : angle 1.63505 ( 36) link_ALPHA1-6 : bond 0.00530 ( 9) link_ALPHA1-6 : angle 2.18707 ( 27) link_BETA1-4 : bond 0.00511 ( 21) link_BETA1-4 : angle 2.02910 ( 63) link_NAG-ASN : bond 0.00676 ( 12) link_NAG-ASN : angle 2.65349 ( 36) *********************** 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 245 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.8613 (m-90) cc_final: 0.8389 (m-90) REVERT: B 584 GLU cc_start: 0.8280 (tp30) cc_final: 0.8041 (tp30) REVERT: C 82 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 90 ASP cc_start: 0.8461 (m-30) cc_final: 0.8249 (m-30) REVERT: G 530 MET cc_start: 0.8160 (mmm) cc_final: 0.7896 (mmm) REVERT: H 90 ASP cc_start: 0.8421 (m-30) cc_final: 0.8060 (m-30) REVERT: H 101 TRP cc_start: 0.8578 (t-100) cc_final: 0.8131 (t-100) REVERT: I 64 PHE cc_start: 0.6112 (m-80) cc_final: 0.5641 (m-10) REVERT: I 72 THR cc_start: 0.7021 (m) cc_final: 0.6695 (p) REVERT: K 95 MET cc_start: 0.8285 (ttm) cc_final: 0.7991 (ttm) REVERT: K 112 TRP cc_start: 0.8277 (t-100) cc_final: 0.8068 (t-100) REVERT: K 359 ILE cc_start: 0.6826 (mt) cc_final: 0.6624 (mt) REVERT: K 475 MET cc_start: 0.7443 (tpt) cc_final: 0.7027 (tpp) REVERT: M 47 TRP cc_start: 0.8310 (t60) cc_final: 0.7861 (t60) REVERT: M 48 MET cc_start: 0.8063 (mmm) cc_final: 0.7606 (mmm) REVERT: M 101 TRP cc_start: 0.8694 (t-100) cc_final: 0.8202 (t-100) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1112 time to fit residues: 44.9017 Evaluate side-chains 183 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.119831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108676 restraints weight = 48194.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105364 restraints weight = 102024.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.104576 restraints weight = 80234.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104136 restraints weight = 88963.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104410 restraints weight = 57038.852| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 20505 Z= 0.291 Angle : 0.855 13.121 28020 Z= 0.430 Chirality : 0.051 0.275 3311 Planarity : 0.005 0.078 3441 Dihedral : 10.610 66.705 3976 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.11 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.15), residues: 2442 helix: -1.01 (0.27), residues: 348 sheet: -1.19 (0.19), residues: 663 loop : -2.00 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 298 TYR 0.021 0.002 TYR A 191 PHE 0.022 0.003 PHE K 93 TRP 0.080 0.003 TRP K 96 HIS 0.008 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00691 (20396) covalent geometry : angle 0.83209 (27735) SS BOND : bond 0.00998 ( 42) SS BOND : angle 2.08838 ( 84) hydrogen bonds : bond 0.04954 ( 583) hydrogen bonds : angle 6.46250 ( 1557) link_ALPHA1-2 : bond 0.00419 ( 13) link_ALPHA1-2 : angle 2.54838 ( 39) link_ALPHA1-3 : bond 0.00925 ( 12) link_ALPHA1-3 : angle 1.61890 ( 36) link_ALPHA1-6 : bond 0.00669 ( 9) link_ALPHA1-6 : angle 2.05245 ( 27) link_BETA1-4 : bond 0.00477 ( 21) link_BETA1-4 : angle 1.90079 ( 63) link_NAG-ASN : bond 0.00578 ( 12) link_NAG-ASN : angle 2.57280 ( 36) *********************** 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 241 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.747 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: A 104 MET cc_start: 0.8401 (tpp) cc_final: 0.8057 (tpp) REVERT: A 377 ASN cc_start: 0.8915 (t0) cc_final: 0.8713 (t0) REVERT: B 584 GLU cc_start: 0.8265 (tp30) cc_final: 0.8049 (tp30) REVERT: D 72 THR cc_start: 0.7281 (m) cc_final: 0.6817 (p) REVERT: F 165 ILE cc_start: 0.8865 (mm) cc_final: 0.8623 (mm) REVERT: F 359 ILE cc_start: 0.7303 (mt) cc_final: 0.7096 (mt) REVERT: H 90 ASP cc_start: 0.8390 (m-30) cc_final: 0.8067 (m-30) REVERT: H 101 TRP cc_start: 0.8628 (t-100) cc_final: 0.8193 (t-100) REVERT: I 64 PHE cc_start: 0.6196 (m-80) cc_final: 0.5856 (m-10) REVERT: I 72 THR cc_start: 0.6989 (m) cc_final: 0.6690 (p) REVERT: K 95 MET cc_start: 0.8228 (ttm) cc_final: 0.7946 (ttm) REVERT: K 107 ASP cc_start: 0.7674 (m-30) cc_final: 0.7243 (t0) REVERT: K 165 ILE cc_start: 0.8901 (mm) cc_final: 0.8696 (mm) REVERT: K 359 ILE cc_start: 0.6939 (mt) cc_final: 0.6719 (mt) REVERT: L 655 LYS cc_start: 0.8647 (pptt) cc_final: 0.8205 (pptt) REVERT: M 2 VAL cc_start: 0.6954 (t) cc_final: 0.6467 (t) REVERT: M 47 TRP cc_start: 0.8281 (t60) cc_final: 0.7761 (t60) REVERT: M 48 MET cc_start: 0.8038 (mmm) cc_final: 0.7581 (mmm) REVERT: M 101 TRP cc_start: 0.8773 (t-100) cc_final: 0.8165 (t-100) REVERT: N 72 THR cc_start: 0.7264 (m) cc_final: 0.6900 (p) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1129 time to fit residues: 45.0128 Evaluate side-chains 182 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 223 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 212 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 575 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.113682 restraints weight = 47234.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111084 restraints weight = 93769.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109734 restraints weight = 70017.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.109828 restraints weight = 75716.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109989 restraints weight = 49318.362| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20505 Z= 0.146 Angle : 0.721 13.039 28020 Z= 0.361 Chirality : 0.047 0.215 3311 Planarity : 0.004 0.073 3441 Dihedral : 9.274 58.627 3976 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.39 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.16), residues: 2442 helix: -0.35 (0.29), residues: 333 sheet: -1.15 (0.19), residues: 654 loop : -1.77 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 298 TYR 0.023 0.002 TYR N 93 PHE 0.010 0.001 PHE M 114 TRP 0.063 0.003 TRP K 96 HIS 0.008 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00333 (20396) covalent geometry : angle 0.70211 (27735) SS BOND : bond 0.00528 ( 42) SS BOND : angle 1.60795 ( 84) hydrogen bonds : bond 0.04083 ( 583) hydrogen bonds : angle 6.04856 ( 1557) link_ALPHA1-2 : bond 0.00337 ( 13) link_ALPHA1-2 : angle 2.16783 ( 39) link_ALPHA1-3 : bond 0.01105 ( 12) link_ALPHA1-3 : angle 1.39527 ( 36) link_ALPHA1-6 : bond 0.00909 ( 9) link_ALPHA1-6 : angle 1.81539 ( 27) link_BETA1-4 : bond 0.00442 ( 21) link_BETA1-4 : angle 1.47257 ( 63) link_NAG-ASN : bond 0.00418 ( 12) link_NAG-ASN : angle 2.25063 ( 36) *********************** 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 248 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8178 (tpp) cc_final: 0.7810 (tpp) REVERT: A 377 ASN cc_start: 0.8843 (t0) cc_final: 0.8580 (t0) REVERT: B 584 GLU cc_start: 0.8115 (tp30) cc_final: 0.7905 (tp30) REVERT: C 90 ASP cc_start: 0.8563 (m-30) cc_final: 0.8152 (m-30) REVERT: D 72 THR cc_start: 0.7116 (m) cc_final: 0.6736 (p) REVERT: H 2 VAL cc_start: 0.7132 (t) cc_final: 0.6850 (t) REVERT: H 101 TRP cc_start: 0.8593 (t-100) cc_final: 0.8132 (t-100) REVERT: I 64 PHE cc_start: 0.6082 (m-80) cc_final: 0.5785 (m-10) REVERT: I 72 THR cc_start: 0.6603 (m) cc_final: 0.6363 (p) REVERT: K 107 ASP cc_start: 0.7516 (m-30) cc_final: 0.7250 (t0) REVERT: K 377 ASN cc_start: 0.8813 (t0) cc_final: 0.8606 (t0) REVERT: K 433 CYS cc_start: 0.7261 (t) cc_final: 0.7044 (t) REVERT: M 2 VAL cc_start: 0.7030 (t) cc_final: 0.6624 (t) REVERT: M 47 TRP cc_start: 0.7869 (t60) cc_final: 0.7426 (t60) REVERT: M 48 MET cc_start: 0.7934 (mmm) cc_final: 0.7512 (mmm) REVERT: M 101 TRP cc_start: 0.8724 (t-100) cc_final: 0.8080 (t-100) REVERT: N 64 PHE cc_start: 0.5987 (m-80) cc_final: 0.5539 (m-10) REVERT: N 72 THR cc_start: 0.6986 (m) cc_final: 0.6720 (p) REVERT: N 88 TYR cc_start: 0.5889 (m-10) cc_final: 0.5633 (m-10) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1085 time to fit residues: 44.4187 Evaluate side-chains 180 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 131 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 220 optimal weight: 0.0980 chunk 105 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** G 575 GLN K 195 ASN K 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112902 restraints weight = 48086.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.111007 restraints weight = 99324.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109537 restraints weight = 74509.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109613 restraints weight = 88762.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109490 restraints weight = 61026.542| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20505 Z= 0.141 Angle : 0.701 12.583 28020 Z= 0.352 Chirality : 0.046 0.217 3311 Planarity : 0.004 0.069 3441 Dihedral : 8.386 59.672 3976 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.53 % Rotamer: Outliers : 0.05 % Allowed : 0.98 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.16), residues: 2442 helix: -0.06 (0.30), residues: 330 sheet: -0.79 (0.20), residues: 639 loop : -1.64 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 588 TYR 0.030 0.001 TYR F 217 PHE 0.010 0.001 PHE A 233 TRP 0.060 0.002 TRP K 96 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00324 (20396) covalent geometry : angle 0.68277 (27735) SS BOND : bond 0.00547 ( 42) SS BOND : angle 1.62971 ( 84) hydrogen bonds : bond 0.03817 ( 583) hydrogen bonds : angle 5.88057 ( 1557) link_ALPHA1-2 : bond 0.00302 ( 13) link_ALPHA1-2 : angle 2.08309 ( 39) link_ALPHA1-3 : bond 0.01064 ( 12) link_ALPHA1-3 : angle 1.31808 ( 36) link_ALPHA1-6 : bond 0.00940 ( 9) link_ALPHA1-6 : angle 1.73839 ( 27) link_BETA1-4 : bond 0.00452 ( 21) link_BETA1-4 : angle 1.35493 ( 63) link_NAG-ASN : bond 0.00371 ( 12) link_NAG-ASN : angle 2.19762 ( 36) *********************** 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 248 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8003 (tpp) cc_final: 0.7570 (tpp) REVERT: A 377 ASN cc_start: 0.8828 (t0) cc_final: 0.8530 (t0) REVERT: B 584 GLU cc_start: 0.8131 (tp30) cc_final: 0.7910 (tp30) REVERT: C 90 ASP cc_start: 0.8473 (m-30) cc_final: 0.8110 (m-30) REVERT: D 72 THR cc_start: 0.7120 (m) cc_final: 0.6755 (p) REVERT: D 93 TYR cc_start: 0.8013 (t80) cc_final: 0.7427 (t80) REVERT: F 107 ASP cc_start: 0.7373 (m-30) cc_final: 0.7090 (t70) REVERT: G 530 MET cc_start: 0.8237 (mmm) cc_final: 0.7997 (mmt) REVERT: H 63 LYS cc_start: 0.8510 (pttp) cc_final: 0.7972 (ttpp) REVERT: H 90 ASP cc_start: 0.8550 (m-30) cc_final: 0.8123 (m-30) REVERT: H 101 TRP cc_start: 0.8566 (t-100) cc_final: 0.8058 (t-100) REVERT: I 64 PHE cc_start: 0.6035 (m-80) cc_final: 0.5601 (m-10) REVERT: I 72 THR cc_start: 0.6750 (m) cc_final: 0.6533 (p) REVERT: K 95 MET cc_start: 0.8306 (ttm) cc_final: 0.7788 (ttm) REVERT: K 258 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: K 377 ASN cc_start: 0.8805 (t0) cc_final: 0.8598 (t0) REVERT: L 530 MET cc_start: 0.8081 (mmm) cc_final: 0.7726 (mpp) REVERT: M 2 VAL cc_start: 0.6970 (t) cc_final: 0.6568 (t) REVERT: M 11 MET cc_start: 0.6974 (mpp) cc_final: 0.6615 (mpp) REVERT: M 101 TRP cc_start: 0.8691 (t-100) cc_final: 0.8049 (t-100) REVERT: N 23 THR cc_start: 0.8036 (p) cc_final: 0.7727 (t) REVERT: N 72 THR cc_start: 0.7041 (m) cc_final: 0.6635 (p) REVERT: N 88 TYR cc_start: 0.5976 (m-10) cc_final: 0.5775 (m-10) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.1086 time to fit residues: 44.7230 Evaluate side-chains 180 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 116 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 210 optimal weight: 0.1980 chunk 187 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** L 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.124964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113810 restraints weight = 47540.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111909 restraints weight = 96040.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.110291 restraints weight = 78107.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110201 restraints weight = 92573.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110053 restraints weight = 69701.638| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20505 Z= 0.153 Angle : 0.698 12.573 28020 Z= 0.353 Chirality : 0.046 0.214 3311 Planarity : 0.004 0.071 3441 Dihedral : 7.985 58.327 3976 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.16), residues: 2442 helix: -0.07 (0.30), residues: 330 sheet: -0.76 (0.20), residues: 663 loop : -1.64 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.025 0.002 TYR N 93 PHE 0.012 0.001 PHE K 176 TRP 0.082 0.003 TRP A 96 HIS 0.007 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00356 (20396) covalent geometry : angle 0.67926 (27735) SS BOND : bond 0.00674 ( 42) SS BOND : angle 1.83509 ( 84) hydrogen bonds : bond 0.03830 ( 583) hydrogen bonds : angle 5.83179 ( 1557) link_ALPHA1-2 : bond 0.00340 ( 13) link_ALPHA1-2 : angle 2.03373 ( 39) link_ALPHA1-3 : bond 0.00992 ( 12) link_ALPHA1-3 : angle 1.29656 ( 36) link_ALPHA1-6 : bond 0.00941 ( 9) link_ALPHA1-6 : angle 1.72254 ( 27) link_BETA1-4 : bond 0.00413 ( 21) link_BETA1-4 : angle 1.32949 ( 63) link_NAG-ASN : bond 0.00350 ( 12) link_NAG-ASN : angle 2.15721 ( 36) *********************** 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 246 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8367 (tpp) cc_final: 0.7948 (tpp) REVERT: A 112 TRP cc_start: 0.8427 (t-100) cc_final: 0.8183 (t-100) REVERT: A 377 ASN cc_start: 0.8849 (t0) cc_final: 0.8572 (t0) REVERT: B 584 GLU cc_start: 0.8180 (tp30) cc_final: 0.7967 (tp30) REVERT: C 90 ASP cc_start: 0.8579 (m-30) cc_final: 0.8231 (m-30) REVERT: D 10 VAL cc_start: 0.5276 (p) cc_final: 0.4900 (t) REVERT: D 72 THR cc_start: 0.6926 (m) cc_final: 0.6601 (p) REVERT: D 93 TYR cc_start: 0.7961 (t80) cc_final: 0.7387 (t80) REVERT: F 95 MET cc_start: 0.8611 (ttt) cc_final: 0.8363 (ttm) REVERT: F 107 ASP cc_start: 0.7289 (m-30) cc_final: 0.7034 (t70) REVERT: F 433 CYS cc_start: 0.7349 (t) cc_final: 0.7052 (t) REVERT: H 90 ASP cc_start: 0.8458 (m-30) cc_final: 0.8084 (m-30) REVERT: H 101 TRP cc_start: 0.8542 (t-100) cc_final: 0.8135 (t-100) REVERT: I 64 PHE cc_start: 0.5989 (m-80) cc_final: 0.5605 (m-80) REVERT: I 72 THR cc_start: 0.6537 (m) cc_final: 0.6261 (p) REVERT: K 377 ASN cc_start: 0.8874 (t0) cc_final: 0.8651 (t0) REVERT: M 2 VAL cc_start: 0.6963 (t) cc_final: 0.6491 (t) REVERT: M 101 TRP cc_start: 0.8720 (t-100) cc_final: 0.8092 (t-100) REVERT: N 23 THR cc_start: 0.7893 (p) cc_final: 0.7611 (t) REVERT: N 72 THR cc_start: 0.6944 (m) cc_final: 0.6568 (p) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1210 time to fit residues: 48.7327 Evaluate side-chains 188 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 55 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** I 16 GLN K 241 ASN L 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111356 restraints weight = 48318.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109929 restraints weight = 104134.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108202 restraints weight = 78781.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107961 restraints weight = 91866.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108066 restraints weight = 60705.468| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20505 Z= 0.199 Angle : 0.745 12.536 28020 Z= 0.377 Chirality : 0.047 0.213 3311 Planarity : 0.005 0.071 3441 Dihedral : 8.039 59.900 3976 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.72 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.16), residues: 2442 helix: -0.17 (0.30), residues: 330 sheet: -0.81 (0.20), residues: 672 loop : -1.75 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 298 TYR 0.026 0.002 TYR I 93 PHE 0.014 0.002 PHE K 176 TRP 0.066 0.003 TRP A 96 HIS 0.006 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00473 (20396) covalent geometry : angle 0.72566 (27735) SS BOND : bond 0.00592 ( 42) SS BOND : angle 1.87558 ( 84) hydrogen bonds : bond 0.04157 ( 583) hydrogen bonds : angle 5.95963 ( 1557) link_ALPHA1-2 : bond 0.00305 ( 13) link_ALPHA1-2 : angle 2.14316 ( 39) link_ALPHA1-3 : bond 0.00932 ( 12) link_ALPHA1-3 : angle 1.36159 ( 36) link_ALPHA1-6 : bond 0.00862 ( 9) link_ALPHA1-6 : angle 1.74998 ( 27) link_BETA1-4 : bond 0.00425 ( 21) link_BETA1-4 : angle 1.40278 ( 63) link_NAG-ASN : bond 0.00399 ( 12) link_NAG-ASN : angle 2.23990 ( 36) ********************** 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 232 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.803 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 69 TRP cc_start: 0.6642 (p-90) cc_final: 0.6077 (p-90) REVERT: A 104 MET cc_start: 0.8143 (tpp) cc_final: 0.7698 (tpp) REVERT: A 377 ASN cc_start: 0.8869 (t0) cc_final: 0.8587 (t0) REVERT: B 530 MET cc_start: 0.8234 (mmm) cc_final: 0.7906 (mpp) REVERT: C 63 LYS cc_start: 0.8551 (pttt) cc_final: 0.8343 (pttm) REVERT: C 90 ASP cc_start: 0.8652 (m-30) cc_final: 0.8188 (m-30) REVERT: D 10 VAL cc_start: 0.5048 (p) cc_final: 0.4692 (t) REVERT: D 72 THR cc_start: 0.6978 (m) cc_final: 0.6561 (p) REVERT: D 93 TYR cc_start: 0.8091 (t80) cc_final: 0.7533 (t80) REVERT: F 95 MET cc_start: 0.8550 (ttt) cc_final: 0.8191 (ttm) REVERT: F 165 ILE cc_start: 0.8908 (mm) cc_final: 0.8649 (mm) REVERT: H 90 ASP cc_start: 0.8598 (m-30) cc_final: 0.8119 (m-30) REVERT: H 101 TRP cc_start: 0.8567 (t-100) cc_final: 0.8149 (t-100) REVERT: I 64 PHE cc_start: 0.5941 (m-80) cc_final: 0.5534 (m-10) REVERT: K 359 ILE cc_start: 0.6786 (mt) cc_final: 0.6580 (mt) REVERT: K 377 ASN cc_start: 0.8958 (t0) cc_final: 0.8739 (t0) REVERT: L 530 MET cc_start: 0.8069 (mmm) cc_final: 0.7713 (mpp) REVERT: M 2 VAL cc_start: 0.6893 (t) cc_final: 0.6582 (t) REVERT: M 82 GLU cc_start: 0.7708 (tp30) cc_final: 0.7386 (tm-30) REVERT: M 101 TRP cc_start: 0.8817 (t-100) cc_final: 0.8184 (t-100) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1133 time to fit residues: 43.5050 Evaluate side-chains 178 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 35 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 231 optimal weight: 0.0010 chunk 193 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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** I 16 GLN I 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.125819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.114231 restraints weight = 46580.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.112073 restraints weight = 94844.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.110782 restraints weight = 68050.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.110821 restraints weight = 69424.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110806 restraints weight = 48186.651| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20505 Z= 0.130 Angle : 0.685 12.625 28020 Z= 0.347 Chirality : 0.045 0.205 3311 Planarity : 0.004 0.073 3441 Dihedral : 7.339 57.644 3976 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.83 % Favored : 94.92 % Rotamer: Outliers : 0.05 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.16), residues: 2442 helix: -0.49 (0.28), residues: 363 sheet: -0.67 (0.20), residues: 672 loop : -1.63 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 38 TYR 0.025 0.001 TYR N 93 PHE 0.011 0.001 PHE A 233 TRP 0.054 0.002 TRP A 96 HIS 0.004 0.001 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00291 (20396) covalent geometry : angle 0.66892 (27735) SS BOND : bond 0.00475 ( 42) SS BOND : angle 1.61933 ( 84) hydrogen bonds : bond 0.03680 ( 583) hydrogen bonds : angle 5.73871 ( 1557) link_ALPHA1-2 : bond 0.00320 ( 13) link_ALPHA1-2 : angle 1.92955 ( 39) link_ALPHA1-3 : bond 0.01036 ( 12) link_ALPHA1-3 : angle 1.21253 ( 36) link_ALPHA1-6 : bond 0.00960 ( 9) link_ALPHA1-6 : angle 1.67395 ( 27) link_BETA1-4 : bond 0.00431 ( 21) link_BETA1-4 : angle 1.21058 ( 63) link_NAG-ASN : bond 0.00336 ( 12) link_NAG-ASN : angle 2.07079 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.06 seconds wall clock time: 39 minutes 12.33 seconds (2352.33 seconds total)